Re: [gmx-users] Zinc (Zn) parameters
Hi Ramon As Tsjerk already mentioned, its generally not that easy with such an "exotic" metal. Depending on the question you want to get answered, certain aspects should be regarded. If the zinc is just keeping the structure in the correct conformation, and is not directly included in the region of interest, the probably easiest way is to use the bonded method, where you simply introduce bonds, which keep the ZN in place (due to LINCS or SHAKE). A harmonic potential didn't work here (for me). However, if this is not possible because it resides e.g. in a catalytic center of interest, its not that easy. The cationic dummy method is probably hard to apply, because the construction of virtual particles in GROMACS depends on at least two real particles. This is obviously not true for one ZN atom. Therefore, the best you can do is, using Tsjerks hint and compute the charge on your ZN in its environment via QM and see, if it remains, where it should. I observed, that ZN likes to leave its place, when complexed to 2 CYS and 2 HIS, given a charge of ~ 0.7. Maybe, also dependent on your interest, QM/MM could help here. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2305 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Ramon Crehuet wrote: Dear Gromacs users, I am planing to do MD of an enzyme that has a Zn in its active site. Up to now I have used QM/MM or ONIOM approaches but now I need to perform a long MD and would like to model the Zn with MM, preferably in OPLS. I know that there are three possible approaches: Bonded, nonbonded and cationic dummy atom. I have seen a thread, where Maik Goette said that onyl the bonded approach worked. I would like to know in more detail what kind of problems could I encounter. What does "not work" imply? Weeks of unreliable calculations...? I would also be very grateful if people working in this area could send me some reference publications, in particular of what can be done with Gromacs. I have only found: "Zinc binding in proteins and solution: A simple but accurate nonbonded representation" Roland H. Stote, Martin Karplus, 1995. Thanks in advance, Ramon ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange dV/dl profile in free energy calculation
Hi Always hard to tell, cause one doesn't know, if your parameters are correct ;) Anyway, the LJ-part always looks a bit unintuitive, probably due to softcore. I saw similar curves in my base-deletions. I think, you can trust the curve. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2305 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: Hello everyone, Sorry if you get this twice. It seems to me that the previous message didn't go through. I'm computing the binding free energy of DNA bases (just the base, no sugar, no phosphate) on a carbon nanotube following the prescirption of the Dill group Wiki (http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial) and the Boresch paper (J. Phys. Chem. B., 107, 9535, 2003). I split my calculation up into two parts. In the first part, I turn off all the charges in my DNA base (guanine in this case). In the second part, I turn off all the LJ parameters. I run MD at each lambda value for 15 ns. An image of the dV/dl plot obtained from the previous simulations is located here: http://dept.physics.upenn.edu/~robertjo/public_files/gmx/dvdl.jpg The error bars are included in the graph (they are very small...less than 1 kJ/mol in all cases). My concern is the dV/dl curve for turning off the LJ parameters (i.e. making the base "disappear") looks fairly strange. First it increases and then decreases to a minimum value at lambda=0.8, and then increases again. This looks significantly different than the identical curve for disappearing a methane molecule in water: http://dept.physics.upenn.edu/~robertjo/public_files/gmx/dgdl_methane.jpg The methane calculation followed the steps discussed in the Dill group Wiki and agrees with the result reported there. Is there anyone who has some experience performing these calculations that can comment on my curve for the DNA base? Does my curve look reasonable? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Free energy of discharging and then recharging not zero
Hi Robert I wouldn't expect that either. Morphing G to A should yield quite reasonable results, cause you just have few dummies in your system. The process, you describe is the way, one would think of, yes. Just to get you right. Are you swithing off charges of a whole base or nucleotide? In the case of a nucleotide, you morph away one netto charge. That could be problematic with PME (?). Maybe trying reaction field could help here. Now, if you turn off the charges of the base and then turn it on again, both contributions should actually lead to the same values, as David said. As long, as no dummies are involved, everything should run smooth. I suggest, you simply do position restrained simulations at the discrete lambda steps, when turning on/off your charges. Maybe, they converge faster then. This would indicate a sampling problem, indeed. For a purine to pyrimidine morph (or vice versa), I'm still convinced, that you would have to sample for ages to get a converged system, though. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: Hi Maik, That's exactly what I'm attempting to do...morph G to A etc. All I'm doing here is turning off the charges of G and then turning them on again. Wouldn't you do this anyway in the morph step? Wouldn't the process go something like: Turn off charges -> Morph LJ parameters -> Turn on charges. It seems like I've got to be doing something wrong. I can't believe that simply turning off/on the charges would drastically perturb the entire system and prevent convergence. Bob On Thu, May 8, 2008 at 6:12 AM, Maik Goette <[EMAIL PROTECTED]> wrote: Hi Robert Sounds familiar to me. I also tried to compute free energy differences by letting whole bases appear/disappear. I ran into the same problems and haven't found a solution yet. Probably the perturbation is too large to gain converged results. My solution was stopping those simulations. This doesn't sound promising, I know, but actually, I fear, there is no proper solution. Maybe you should morph G to A or T to C or something like that, where just a few atoms have to be perturbed. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: Hello everyone, I'm trying to calculate the free energy of binding of DNA bases on a carbon nanotube. I'm running some tests to make sure that I'm doing everything correctly. One thing I tried was turning off all the atom charges of the DNA base and then turning them back on again. Theoretically, the free energy changes of these two processes should be equal and opposite and thus sum to zero. However, this is not what I'm finding. For guanine, I get a free energy change of 648 kJ/mol and -618 kJ/mol for turning off and turning on the charges, respectively. Obviously, they are not equal by 30 kJ/mol, which seems pretty big. I have done some error estimation using the g_analyze -ee program. One thing I find strange is that the error estimates in dV/dl for TURNING ON the charges is large (over 2) and do not even converge for a 7.5 ns simulation. In contrast, the error in dV/dl for TURNING OFF the charges converges extremely quickly (using small block sizes of 50 or less) and is smaller at 0.3. So it seems like I have some sampling problems with the TURNING ON portion. Is there some reason why you must sample a longer trajectory when turning on the charges? I'm following the procedures of http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial Does anyone know the reason for the discrepancy between these two (seemingly identical) processes? Thanks, Bob ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the
Re: [gmx-users] Free energy of discharging and then recharging not zero
Hi Robert Sounds familiar to me. I also tried to compute free energy differences by letting whole bases appear/disappear. I ran into the same problems and haven't found a solution yet. Probably the perturbation is too large to gain converged results. My solution was stopping those simulations. This doesn't sound promising, I know, but actually, I fear, there is no proper solution. Maybe you should morph G to A or T to C or something like that, where just a few atoms have to be perturbed. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: Hello everyone, I'm trying to calculate the free energy of binding of DNA bases on a carbon nanotube. I'm running some tests to make sure that I'm doing everything correctly. One thing I tried was turning off all the atom charges of the DNA base and then turning them back on again. Theoretically, the free energy changes of these two processes should be equal and opposite and thus sum to zero. However, this is not what I'm finding. For guanine, I get a free energy change of 648 kJ/mol and -618 kJ/mol for turning off and turning on the charges, respectively. Obviously, they are not equal by 30 kJ/mol, which seems pretty big. I have done some error estimation using the g_analyze -ee program. One thing I find strange is that the error estimates in dV/dl for TURNING ON the charges is large (over 2) and do not even converge for a 7.5 ns simulation. In contrast, the error in dV/dl for TURNING OFF the charges converges extremely quickly (using small block sizes of 50 or less) and is smaller at 0.3. So it seems like I have some sampling problems with the TURNING ON portion. Is there some reason why you must sample a longer trajectory when turning on the charges? I'm following the procedures of http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial Does anyone know the reason for the discrepancy between these two (seemingly identical) processes? Thanks, Bob ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Free energy - Hydrogen bond solute-solvent - Ethanol as an example.
Hi I'm not to sure about how Berk exactly did that. But, if I understood that correctly, he let things vanish (which is for sure the better method, than letting things appear). If he did that, he computed the DEsolvation free energy. This actually is the inverse of the solvation free energy. Therefore, I think, you have to switch the sign of your calculations and you're fine. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Eudes Fileti wrote: Hello to all I have tried to reproduce the hydration free energy (TI) of the ethanol from Hess and van der Vegt (JPCB, 110, 17616). The value I have obtained is around 20kJ/mol while the reference value is -20.1kJ/mol (if not the sign ...). If someone can help me find the mistake I would be very grateful. Below are the simulation details. I followed the protocol of the paper, Berk: I used 47 lambda values (because of hydrogen bonds between solute-solvent) (dense near lambda=0 and between 0.46 and 0.72). I am turning off the LJ and Coulomb terms separately. Softcore (alpha = 0.5, power = 1), OPLS-AA Timestep = 2fs, sd = integrator, PME constrained = none trajectories = 40ps (NVT) (I know that is small, but I looking for qualitative results) after 20ps of equilibration (NPT). I have found a value of -4.8kJ/mol for the DeltaG(vacuum) (relative to mutate the ethanol to dummy in vacuum). My dv/dl curve (for DeltaG(water) is below. Should I expect this form? I think there are many "high" positive values. The numerical integration is 15.9kJ. So, DG(hyd) = DG(wat) - DG(vac) = 15.9 - (-4.8) = 20.7kJ I believe that this protocol is OK (but I want to confirm that). @title "dG/d\8l\4" @xaxis label "Time (ps)" @yaxis label "dG/d\8l\4 (kJ mol\S-1\N [\8l\4]\S-1\N)" @TYPE xy 0.000 4.431073e+02 0.005 3.660083e+02 0.010 2.987275e+02 0.015 2.023206e+02 0.000 4.431073e+02 0.005 3.660083e+02 0.010 2.987275e+02 0.015 2.023206e+02 0.020 1.905198e+02 0.030 1.086573e+02 0.040 4.217960e+01 0.050 4.101856e+01 0.060 2.314358e+01 0.070 2.223774e+01 0.080 2.669019e+01 0.090 1.696131e+01 0.100 6.089735e+00 0.110 9.569030e+00 0.120 1.505562e+01 0.130 2.785974e+00 0.140 2.440906e+00 0.150 3.050463e+00 0.160 8.578429e-01 0.200 3.577259e+00 0.240 -3.532969e+00 0.280 5.842623e+00 0.320 7.912565e+00 0.360 9.322502e+00 0.400 -2.930754e+00 0.440 2.797944e+00 0.460 5.113900e+00 0.480 -3.919665e+00 0.500 -9.000282e+00 0.520 -7.636168e+00 0.540 -7.574299e+00 0.560 -2.144124e+01 0.580 -6.618514e+00 0.600 -2.755925e+01 0.620 -1.491331e+01 0.640 -2.541398e+01 0.660 -5.213154e+01 0.680 -2.364612e+01 0.700 -2.535817e+01 0.720 -7.767502e+00 0.760 -1.096362e+01 0.800 1.136031e+01 0.840 2.883933e+01 0.880 4.465743e+01 0.920 5.461566e+01 0.960 6.882000e+01 1.000 7.673736e+01 -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: combining differently-generated force-fields
Hi This IS a textbook-chapter. It seems very fresh. Just found it here on Bert's desk. After a very rough inspection, I don't expect anything new or any breakthrough, though. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Thanks Soo Mei, that might be interesting. I couldn't access it either. I think it is a book (http://www.springer.com/series/7651) MacKerell's website indicates that it is not yet in press, although I am not sure how recently that was updated: Guvench, O. and MacKerell, A.D., Jr., ?Comparison of protein force fields for molecular dynamics simulations,? In Molecular Modeling of Proteins, A. Kukol, Editor, Humana Press, Submitted. --original message -- A related reference might be this? Comparison of protein force fields for molecular dynamics simulations. Methods Mol Biol. 2008;443:63-88. Guvench O, Mackerell AD Jr. Not that I've read it yet, because my institute doesn't have access to that journal. Cheers, Soo Mei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] free energy calculation
So, obviously, no one knows how to do that by g_lie. Most people here compute free energies by TI. Do some background reading and find out yourself how it works. Posting mails twice or more won't help you regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ shuai lu wrote: Hi everyone, I want to calculate free energy between protein and ligand by "g_lie" command. So the average Coulomb interaction and average Lennard-Jones interaction of ligand-solvent are need. But I do not know if average Coulomb interaction is the result of "Coul-SR" plus "Coul-14", which are calculated by "g_energy" command, and also if Lennard-Jones interaction is the result of "LJ-SR" plus "LJ-LR" plus "LJ-14". Hence I hope anyone who know about them may help me kindly. Thank you! -- Lu Shuai ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GTP in topology
It means: Include the topology, you got from the PRODRG server as an itp file in your general topology file If you don't know, what I mean, read the manual about including topologies... Btw, more info, more answer regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ s lal badshah wrote: Hi All, I have taken the GTP topology from PRODRG server but now how can I make a connection with my original topology file: As in Errors of Gromacs it is mentioned ==> find a topology file <http://wiki.gromacs.org/index.php/topology_file> for the residue / molecule and include as a .itp file <http://wiki.gromacs.org/index.php/.itp_file>, what does it means? I am using OPLS/aa force field. Regards, Lal badshah. *SYED LAL BADSHAH M.Phil Scholar NCE in Physical Chemistry, University of Peshawar. NWFP,Pakistan. Cell # 03349060632.* Send instant messages to your online friends http://uk.messenger.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] set up topology in free energy calculations
QL, 1. Yes. I'd use version a) because of, the less dummies, the better. 2. Yes 3. Of course, charges have to vanish for dummies, too. Keep the bonded terms. If not, your dummies will "diffuse" away. Yes, your assumption about dummies is right. Actually, I won't use this system for your first perturbation. Take something simpler. Second, as indicated by point 3, you will have to tackle a disappearing netto charge of -1 (depending on the pH of course). This usually is a problem. There were discussions of PME being problematic here. Morphing an ion to counter that charge difference is possible. However, I think this would lead to a very bad equilibrated system and no reasonable results. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ friendli wrote: Dear Gmx users, I am calculating the mutation free energy from amino acid Asp to Asn as a test job for my practice. I have some questions about setting up the topology file. 1, from Asp to Asn mutation, the -CH2-COOH changes to -CH2-CO-NH2 or simply -OH to -NH2. In topology, O <-> N. What about the hydrogens, do I need one or two dummy(DUM) atoms? a), DUM <-> H ; H(of OH) <-> H(of NH2) b), DUM <-> H(of NH2); DUM <-> H(of NH2); H(of OH) to DUM a) or b) should I use? 2, I need to provide the coordinates for the dummy atoms in the .gro file(Asp), right? since otherwise the # of atoms in .top and .gro will mismatch. 3, from the tutorial(methane) I read, the masses of the dummy atom keeps like real atom and the C6 and C12 changes to zero in [atomtypes] to vanish the nonbonded interactions. How to deal with the bonds and the charges for dummy atoms? bonded interactions? I think I am a bit confused by the definition of the dummy atom. I understanding is a dummy atom is a atoms with same mass but no interaction with all other atoms. Is that right? thanks for help and suggestions are appreciate. QL ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Black whole simluations
Thank you Sir If this was fake or not...Me and my dear colleagues had a good laugh, anyway...also about the nice comments. Maybe this inspires: http://www.youtube.com/watch?v=qiSkyEyBczU "Black hole sun, won't you come" Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ roger han wrote: > Dear mister gromacs > > My professor interested in black wholes. How can I put a particle in a box > and set mass to infinity? Which solvent is best choice and could there be > problems with pressure? I'm also not sure about periodic boundaries. Could > two black wholes see each other if box too small? > > Many thanks > > Ben > _ > 聰明搜尋和瀏覽網路的免費工具列 — MSN 搜尋工具列 > http://toolbar.live.com/ > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > . > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] traj.trr
Read the manual... Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ s lal badshah wrote: Dear gromacs users, Hi, In my simulation directory one file is present on the name of traj.trr Is this shows that my mdrun crashed? regards, *SYED LAL BADSHAH M.Phil Scholar NCE in Physical Chemistry, University of Peshawar. NWFP,Pakistan. Cell # 03349060632.* Send instant messages to your online friends http://uk.messenger.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Ki estimation
You can't compare a Ki directly from the MD AFAIK. What you could do is, computing the free energy difference between two ligands and compare it to the difference in Ki (which actually is closely related to the famous Kd), if that helps you Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ V. Tanchuk wrote: Dear Users, I am working Drug – Enzyme Complex. Unfortunately, docking software (AutoDock) was not able to give any resonable results. I have tried to use Gromacs and got a resonable binding. The best results were obtained in the case of simple minimization of the crude AutoDock's results. The question is how to estimate Ki. There is also another problem. I have the best correlation between experimental and calculated results only for the total energy in the case of optimization (it seems that other kids of energy are not available without molecular dynamics, but total or any other energies obtained after molecular dynamics do not correlate). Thank you in advance for your help. Sincerely yours, V. Tanchuk ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with undistribution of water
That "problem" is called periodic boundaries. Try inserting a second bilayer to get, at least on one axis, a water layer between the two lipid layers, if you want to prevent PBC for a part of the waters. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ sudheer babu wrote: Thanks Mr .Justin for your response, I am describing answers for your questions, 1.My box size is 6.0nm in xyz dimensions. 2.The forcefield I am using "ffgmx.itp" for membrane which I downloaded from Pieter Tieleman webiste and deprecated FF for protein. 3 .I inserted protein into membrane by using genbox command. 4. I used force constant 1 on protein. There is no leaking of membrane, the stucture is fine till EM, but in PR the water molecules are moving from one side of the bilyaer to the other side. No water mol between lipid bilyer hydrophobic region. Ok I tell you in clear way, Assume on membrane each side 200 water molecules are there but after equilabration 30 to 50 water molecules are reaching other side , so one side its appearing more rather than other side. But it looks in cubic form how appears in EM but only increasing water molecules on other side. Popc and protein are fine. Will it cause any problem later when I run further simulation by taking this output file.I hope you got my problem. Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange dgdl-value together with lincs
David, Berk, > Hold on, if you are doing this with hardcore, there is a singularity > in dG/dlambda. It won't be numerically integrable so whatever you > compute will be in error. See my recent JCP paper that I referred you > to before. thats what I thought. With the latest patched code, I get really good results for the three-step process and, for the hardcore LJ a deviation, which really comes from the singularities, I guess. Now, the 10ns hardcore slow growth and the 3-step discrete lambda sampling yield perfectly the same number and this is fine. I will now continue with computing the non-equilibrium values for the switching process, but I think, those numbers will be ok, too. > For what it's worth, too, a delta_lambda of 0.02 is insanely fast > "slow growth". agreed ;) This was just for bug tracking issues. The step I will use for production will be slightly smaller :) Thanks for all your help. Btw, cause I already uploaded the pics, here they are: The 1-step hardcore process: http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/tot.png 3-step QQ off: http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/qqoff.png 3-step QQ on: http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/qqon.png 3-step LJ and bonded softcore: http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/vdw_sc.png 3-step LJ and bonded hardcore: http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/vdw_hc.png This actually proofs again the problem of singularities while using hardcore LJ morphs. Anyway, the softcore part looks fine and the sum of the single contributions fits quite well. As I found out recently, the GROMACS version on the cluster I used, was without the november bug fix, so I can't tell which fix helped with the problem. Sorry for that. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ David Mobley wrote: Maik, Assume, you take the interconversion of ethane to methanol in solvent in one step. You sample hardcore at 11 evenly spaced lambda values for, lets say, 2 ns each. You get the dG/dl mean from every run and integrate via simpson to get a total DG. Hold on, if you are doing this with hardcore, there is a singularity in dG/dlambda. It won't be numerically integrable so whatever you compute will be in error. See my recent JCP paper that I referred you to before. I think if you are using hardcore, you *have* to use slow growth and the Jarzynski or Crooks expressions, or do some sort of polynomial fit to the singularity in dG/dlambda and integrate the polynomial. Integrating dG/dlambda directly will simply fail since you can't numerically integrate a singularity. If you're using softcore, you have more options, and simple numerical integration can work. For what it's worth, too, a delta_lambda of 0.02 is insanely fast "slow growth". David ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange dgdl-value together with lincs
Jeroen, I'm aware of that bug and using the 3.3.2_pre, with the bugfix included. Btw, I don't see how to sample "backwards" ;) Probably you mean in the case of slow growth, no? In that case, the problem occurs in both directions. Berk, there are quite a few files (44 in that case). I will sample the system a bit longer (66ns for each case in total) and make a gz-download. Anyway, to me they look normal. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ van Bemmelen wrote: Maik, This is just a hunch, but since you're turning charges on (instead of off) in the third step, maybe this is also a case of bug 175 (http://bugzilla.gromacs.org/show_bug.cgi?id=175). That is, if you're using PME for electrostatics. This bug has been fixed for the CVS version. Another "fix" would be to do all steps in the reverse direction. Greetz, Jeroen Unluckily, both numbers deviate by roughly 10 kJ. I have the feeling, that hydrogen bonding could play a role, but intuitively, I'd say it shouldn't differ in the free energy of both. Thanks again for the help Maik Goette, Dipl. Biol. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange dgdl-value together with lincs
Thanks, Berk I'm also quite sure, that this spike doesn't explain the deviations I see in adding up single DG contributions. Maybe I just bring it up once more: Assume, you take the interconversion of ethane to methanol in solvent in one step. You sample hardcore at 11 evenly spaced lambda values for, lets say, 2 ns each. You get the dG/dl mean from every run and integrate via simpson to get a total DG. Now, you do the same, but split your process into 3. Switching charges to zero, morph the vdw and bondeds, switching charges back on. All hardcore to keep comparability. You take 3x11 lambda snapshots and sample for 666ps each. You do the integration 3 times like above. The sum of these 3 DGs should yield the same DG as the run above, I suppose. Unluckily, both numbers deviate by roughly 10 kJ. I have the feeling, that hydrogen bonding could play a role, but intuitively, I'd say it shouldn't differ in the free energy of both. Thanks again for the help Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Berk Hess wrote: From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] Strange dgdl-value together with lincs Date: Tue, 19 Feb 2008 11:20:14 +0100 Date: Fri, 15 Feb 2008 09:27:24 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] Strange dgdl-value together with lincs Berk, here comes the topology for this run (vdw morph): Its OPLSAA and the hydrogens have bond terms. This is the standard OPLSAA FF for ethane and methanol. Thanks. OK, I found the problem. You have a delta_lambda of 0.02, which is so high that the kinetic energy of the constrained degrees of freedom is no longer negligible. I am not sure if constraints with kinetic energy are formally correct. But anyhow, you had unconstrained_start=yes, which is probably incorrect, since I assume your equilibration run had delta_lambda=0 and therefore in the starting configuration the constraint velocity is zero. The spike in dG/dl therefore corresponds to building up this kinetic energy. Now even if you would set unconstrained_start=no, this would not help, since Gromacs would not put velocities into the constraints at startup. I have managed to fix this in the code (not committed). But when delta_lamda is so large, the is another issue. The coordinates are constrained after the update with lambda of the current step, but the constraints in the updated configuration should actually obey the lengths for the next step. I have to think if things can still be somewhat correct with such a large delta_lambda, before I starting correcting these two issues. Berk. I have now properly fixed this issue in the CVS head branch. The constraint lengths are now exactly correct at every step and with unconstrained_start=no the spike in dG/dl due to the velocity is gone. Note that the error would normally be extreme small, since delta_lambda is normally extremely small. Berk. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] toluene tutorial sc-power value
Fine :) So forget what I wrote before...I mentioned exactly that :) Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi maik I made the calculation with sc-power=2 adding 3 lambda values. Now i get integrating the plot of average free energy for the mutation of toluene in water 0.559 instead of 15,8 in previous calculation. if i combine with the free energy in vacuo i have -3,41 KJ/mol vs (-3,1 KJ/mol exp.). This is quite ok!! :) So the error was a combination of number of points- sc-parameter but for sure number of points are really important for the integration part!!! in the calculation of free energy. . regards geraldine On Fri, February 15, 2008 11:07 am, Maik Goette wrote: I had a veeery short look into the tutorial and found an error. DG_hyd=DG_1-DG_3-DG_2 for the cycle is wrong. The correct cycle would be: DG_1+DG_3=DG_hyd+DG_2 =>DG_hyd=DG_1-DG_2+DG_3 with DG_3 =0 So its: DG_hyd=DG_1-DG_2 instead of DG_hyd=DG_1-DG_3 Anyway, this won't help you, cause the only effect is a change of the sign to +19 and therefore worse. Can you show me the topology, you made? As far as the free energy experts here discussed it, sc-power=2 shouldn't be the lambda-dependance of choice. I can agree to that from my simulations. regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi maik the energy DEltaG_hyd=deltaG_mutation(vacuo)-deltaGmutation(water) for fisrt one deltaG_mutation(vacuo) =-2,85 for second deltaGmutation(water) =15,87 so i found DEltaG_hyd = -19 kj/mol instead of -3,1 kj/mol i'll do a series of calculation with sc-power=2 and see the difference see if there's some significant difference. geraldine On Thu, February 14, 2008 10:57 am, Maik Goette wrote: Hi Now, make sure, that you apply the thermodynamic cycle correctly. I wouldn't wonder about large errors. Depending on the definition of large. Error estimation from free energy calculations can be very tricky. Using mpi shouldn't influence your calculations outcome. Still I don't know the error. How to post the numbers: Exp. value (+error) and your calculated value (+error) ? From those I could tell you if something is terribly wrong or not. :) Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi MaiK, Sorry i forgot the subject. Thank you to have answered this email. This tutorial is about solvation free energy of toluene using thermodynamical cycles. two energies have to be calculated according to this cycle, the hydration energy of toluene and the mutation energy from dummy to toluene in vacuo. For each energy calculation several MD simulation for different lambda value must be performed. in the mdp files given i added the line sc-power=1 and made the calculation. from the file dgdl.xvg obtained for each lambda value i used the g_analyse command to get the average and the estimated error of free energy. i made the plot =f(lambda) for the first part (hydration of toluene) integrated and get the integrated value of the plot and did the same for mutation energy of toluene and made the difference of the two integrated values. I really don't know where the error came from : -version of gromacs, the fact that mpi has been used for the first part and single process for the mutation part (because of shake block problem) won't change anything i guess, I would carefully go through one more time and check why i didn't get the right value. I don't know if this high estimated error is really problematic. regards geraldine On Wed, February 13, 2008 6:19 pm, Maik Goette wrote: Hi First of all: You can be quite happy, if anyone reads a "no subject" mail. sc-power seems to be set to zero in the newer version, in contrast to the old ones, where it was 1 by default. Therefore GROMACS complains. 1 is the value, you should use. I don't know the tutorial, but if you use exactly the files given there (and add sc-power = 1), you should get values, which are close to the experimental one (I guess, cause a tutorial won't make sens
Re: [gmx-users] toluene tutorial sc-power value
hi 10 points is strange ;) 11 is the number with equally spaced points. ANyway, it should suffice to get a more or less proper number. I guess, they use simpsons integration, what should be ok. I compared my scripts results, which uses simpson, with those of xmgrace and they fit. The longer you sample each lambda value and the more lambda values you sample, the better the results, but with this system, I think, 11 lambda values with 1ns each should be enough. Be aware of the fact, that you should cut away a few picoseconds of each dgdl-file for equilibration purposes (100-200). The topology seems not too bad. I'm not used to that forcefield, though. As a general suggestion, its always better to sample many lambda points and each longer, than wasting time with using sc-power=2 :) Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: hi concerning the cycle i saw this error since i started the tutorial, i paid attention to that but as you said it's not that important since my energy value is too high. i'm right now doing the problem again with sc-power=2 and also 10 points is it enough to have an approximate correct value since i have to integrate the average energy plot by xmgrace, i don't know what kind of integration they use, trapezoid? or... it could have an effect if i don't have enough point. but then .. here attached is my top. file. regards geraldine On Fri, February 15, 2008 11:07 am, Maik Goette wrote: I had a veeery short look into the tutorial and found an error. DG_hyd=DG_1-DG_3-DG_2 for the cycle is wrong. The correct cycle would be: DG_1+DG_3=DG_hyd+DG_2 =>DG_hyd=DG_1-DG_2+DG_3 with DG_3 =0 So its: DG_hyd=DG_1-DG_2 instead of DG_hyd=DG_1-DG_3 Anyway, this won't help you, cause the only effect is a change of the sign to +19 and therefore worse. Can you show me the topology, you made? As far as the free energy experts here discussed it, sc-power=2 shouldn't be the lambda-dependance of choice. I can agree to that from my simulations. regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi maik the energy DEltaG_hyd=deltaG_mutation(vacuo)-deltaGmutation(water) for fisrt one deltaG_mutation(vacuo) =-2,85 for second deltaGmutation(water) =15,87 so i found DEltaG_hyd = -19 kj/mol instead of -3,1 kj/mol i'll do a series of calculation with sc-power=2 and see the difference see if there's some significant difference. geraldine On Thu, February 14, 2008 10:57 am, Maik Goette wrote: Hi Now, make sure, that you apply the thermodynamic cycle correctly. I wouldn't wonder about large errors. Depending on the definition of large. Error estimation from free energy calculations can be very tricky. Using mpi shouldn't influence your calculations outcome. Still I don't know the error. How to post the numbers: Exp. value (+error) and your calculated value (+error) ? From those I could tell you if something is terribly wrong or not. :) Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi MaiK, Sorry i forgot the subject. Thank you to have answered this email. This tutorial is about solvation free energy of toluene using thermodynamical cycles. two energies have to be calculated according to this cycle, the hydration energy of toluene and the mutation energy from dummy to toluene in vacuo. For each energy calculation several MD simulation for different lambda value must be performed. in the mdp files given i added the line sc-power=1 and made the calculation. from the file dgdl.xvg obtained for each lambda value i used the g_analyse command to get the average and the estimated error of free energy. i made the plot =f(lambda) for the first part (hydration of toluene) integrated and get the integrated value of the plot and did the same for mutation energy of toluene and made the difference of the two integrated values. I really don't know where the error came from : -version of gromacs, the fact that mpi has been used for the first part and single process for the mutat
Re: [gmx-users] toluene tutorial sc-power value
I had a veeery short look into the tutorial and found an error. DG_hyd=DG_1-DG_3-DG_2 for the cycle is wrong. The correct cycle would be: DG_1+DG_3=DG_hyd+DG_2 =>DG_hyd=DG_1-DG_2+DG_3 with DG_3 =0 So its: DG_hyd=DG_1-DG_2 instead of DG_hyd=DG_1-DG_3 Anyway, this won't help you, cause the only effect is a change of the sign to +19 and therefore worse. Can you show me the topology, you made? As far as the free energy experts here discussed it, sc-power=2 shouldn't be the lambda-dependance of choice. I can agree to that from my simulations. regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi maik the energy DEltaG_hyd=deltaG_mutation(vacuo)-deltaGmutation(water) for fisrt one deltaG_mutation(vacuo) =-2,85 for second deltaGmutation(water) =15,87 so i found DEltaG_hyd = -19 kj/mol instead of -3,1 kj/mol i'll do a series of calculation with sc-power=2 and see the difference see if there's some significant difference. geraldine On Thu, February 14, 2008 10:57 am, Maik Goette wrote: Hi Now, make sure, that you apply the thermodynamic cycle correctly. I wouldn't wonder about large errors. Depending on the definition of large. Error estimation from free energy calculations can be very tricky. Using mpi shouldn't influence your calculations outcome. Still I don't know the error. How to post the numbers: Exp. value (+error) and your calculated value (+error) ? From those I could tell you if something is terribly wrong or not. :) Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi MaiK, Sorry i forgot the subject. Thank you to have answered this email. This tutorial is about solvation free energy of toluene using thermodynamical cycles. two energies have to be calculated according to this cycle, the hydration energy of toluene and the mutation energy from dummy to toluene in vacuo. For each energy calculation several MD simulation for different lambda value must be performed. in the mdp files given i added the line sc-power=1 and made the calculation. from the file dgdl.xvg obtained for each lambda value i used the g_analyse command to get the average and the estimated error of free energy. i made the plot =f(lambda) for the first part (hydration of toluene) integrated and get the integrated value of the plot and did the same for mutation energy of toluene and made the difference of the two integrated values. I really don't know where the error came from : -version of gromacs, the fact that mpi has been used for the first part and single process for the mutation part (because of shake block problem) won't change anything i guess, I would carefully go through one more time and check why i didn't get the right value. I don't know if this high estimated error is really problematic. regards geraldine On Wed, February 13, 2008 6:19 pm, Maik Goette wrote: Hi First of all: You can be quite happy, if anyone reads a "no subject" mail. sc-power seems to be set to zero in the newer version, in contrast to the old ones, where it was 1 by default. Therefore GROMACS complains. 1 is the value, you should use. I don't know the tutorial, but if you use exactly the files given there (and add sc-power = 1), you should get values, which are close to the experimental one (I guess, cause a tutorial won't make sense, if the files don't yield the desired value). Sorry, but more help is hard to give with so few information. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi all, i 'm a beginner in molecular dynamics. I was doing the tutorial of md group, hydration free energy of toluene : http://md.chem.rug.nl/education/Free-Energy_Course/2.hydration-fe.h tml i have some problems regarding the calculation of toluene in water. the thing is that in the examples files equ-10.00.mdp and data-10.00.mdp no sc-power were mentioned and doing the calculation the error files mentioned about sc-power must be >0 so i added this line sc-power=1 to those files. Analyzing the dgdl.xvg fi
Re: [gmx-users] (no subject)
grompp cant find your mdp-file. Please give a subject next time, as well as more detailed information. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Luisa Calvanese wrote: Hello gmx-users, when I try to generate preprocessing binary files (.tpr) using the grompp command the following error message appears: creating statusfile for 1 node... --- Program grompp, VERSION 3.3.2 Source code file: futil.c, line: 345 File input/output error: min0.mdp --- Can you help me? Luisa Messenger Giochi Prenditi una pausa e sfida i tuoi amici a Ladybird su Messenger! <http://messengergiochi.it.msn.com/ladybird.aspx> ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange dgdl-value together with lincs
Berk, here comes the topology for this run (vdw morph): Its OPLSAA and the hydrogens have bond terms. This is the standard OPLSAA FF for ethane and methanol. Thanks. [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_135 1E2M CB 10.0 12.011 opls_1570.0 12.011 2 opls_140 1E2MHB1 10.0 1.008 opls_1560.0 1.008 3 opls_140 1E2MHB2 10.0 1.008 opls_1560.0 1.008 4 opls_140 1E2MHB3 10.0 1.008 opls_1560.0 1.008 5 opls_135 1E2M CA 20.0 12.011 opls_1540.015.9994 6 opls_140 1E2MHA1 20.0 1.008 opls_1550.0 1.008 7 opls_140 1E2MHA2 20.0 1.008 DUM0.0 1.008 8 opls_140 1E2MHA3 20.0 1.008 DUM0.0 1.008 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 0.10900284512.0 0.10900284512.0 1 3 1 0.10900284512.0 0.10900284512.0 1 4 1 0.10900284512.0 0.10900284512.0 1 5 1 0.15290224262.4 0.14100267776.0 5 6 1 0.10900284512.0 0.09450462750.4 5 7 1 0.10900284512.0 0.10900284512.0 5 8 1 0.10900284512.0 0.10900284512.0 [ pairs ] ; aiaj functc0c1c2c3 2 6 1 2 7 1 2 8 1 3 6 1 3 7 1 3 8 1 4 6 1 4 7 1 4 8 1 [ angles ] ; aiajak functc0c1c2 c3 2 1 3 1 107.800 276.144 107.800 276.144 2 1 4 1 107.800 276.144 107.800 276.144 2 1 5 1 110.700 313.800 109.500 292.880 3 1 4 1 107.800 276.144 107.800 276.144 3 1 5 1 110.700 313.800 109.500 292.880 4 1 5 1 110.700 313.800 109.500 292.880 1 5 6 1 110.700 313.800 108.500 460.240 1 5 7 1 110.700 313.800 110.700 313.800 1 5 8 1 110.700 313.800 110.700 313.800 6 5 7 1 107.800 276.144 107.800 276.144 6 5 8 1 107.800 276.144 107.800 276.144 7 5 8 1 107.800 276.144 107.800 276.144 [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 2 1 5 6 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 0.94140 2.82420 0.0 -3.76560 0.0 0.0 2 1 5 7 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 0.62760 1.88280 0.0 -2.51040 0.0 0.0 2 1 5 8 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 0.62760 1.88280 0.0 -2.51040 0.0 0.0 3 1 5 6 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 0.94140 2.82420 0.0 -3.76560 0.0 0.0 3 1 5 7 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 0.62760 1.88280 0.0 -2.51040 0.0 0.0 3 1 5 8 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 0.62760 1.88280 0.0 -2.51040 0.0 0.0 4 1 5 6 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 0.94140 2.82420 0.0 -3.76560 0.0 0.0 4 1 5 7 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 0.62760 1.88280 0.0 -2.51040 0.0 0.0 4 1 5 8 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 0.62760 1.88280 0.0 -2.51040 0.0 0.0 Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Berk Hess wrote: I assume your are using a united atom model. What are the bonded parameters for the methanol H in the ethane topology? Does it have the no
[gmx-users] Strange dgdl-value together with lincs
Hi While trying to find, whats wrong with some of my free energy calculation, I stumbled upon a strange thing, I don't understand. I'm simulating the interconversion of ethane to methanol in vacuum. I'm splitting the process into 3 steps: 1. charge of perturbed atoms -> 0 2. morph of LJ-parameters and bonds 3. charge of perturbed atoms -> B-state values Each system is morphed with 1 fs timestep and within 50 steps. The total energies at the "borders" of the simulations (qqoff/vdw, vdw/qqon, qqon/vdw and vdw/qqoff) perfectly match and show no jump; the following simulation always got energies and velocities from the one before. Now, when running the LJ morph A->B with lincs, the dgdl looks like this: http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_lincs_01.png For B->A: http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_lincs_10.png Doing both without lincs yields: http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_nolincs_01.png For B->A http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_nolincs_10.png I find this spike in the first step extremely strange. Additionally it only occurs, when using shake or lincs as constraint solver. I guess, in a longer process it will contribute to the integral in a neglectable manner, but maybe theres some bug. The latest CVS shows the same behaviour. Any comments on that? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] toluene tutorial sc-power value
Hi Now, make sure, that you apply the thermodynamic cycle correctly. I wouldn't wonder about large errors. Depending on the definition of large. Error estimation from free energy calculations can be very tricky. Using mpi shouldn't influence your calculations outcome. Still I don't know the error. How to post the numbers: Exp. value (+error) and your calculated value (+error) ? From those I could tell you if something is terribly wrong or not. :) Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi MaiK, Sorry i forgot the subject. Thank you to have answered this email. This tutorial is about solvation free energy of toluene using thermodynamical cycles. two energies have to be calculated according to this cycle, the hydration energy of toluene and the mutation energy from dummy to toluene in vacuo. For each energy calculation several MD simulation for different lambda value must be performed. in the mdp files given i added the line sc-power=1 and made the calculation. from the file dgdl.xvg obtained for each lambda value i used the g_analyse command to get the average and the estimated error of free energy. i made the plot =f(lambda) for the first part (hydration of toluene) integrated and get the integrated value of the plot and did the same for mutation energy of toluene and made the difference of the two integrated values. I really don't know where the error came from : -version of gromacs, the fact that mpi has been used for the first part and single process for the mutation part (because of shake block problem) won't change anything i guess, I would carefully go through one more time and check why i didn't get the right value. I don't know if this high estimated error is really problematic. regards geraldine On Wed, February 13, 2008 6:19 pm, Maik Goette wrote: Hi First of all: You can be quite happy, if anyone reads a "no subject" mail. sc-power seems to be set to zero in the newer version, in contrast to the old ones, where it was 1 by default. Therefore GROMACS complains. 1 is the value, you should use. I don't know the tutorial, but if you use exactly the files given there (and add sc-power = 1), you should get values, which are close to the experimental one (I guess, cause a tutorial won't make sense, if the files don't yield the desired value). Sorry, but more help is hard to give with so few information. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi all, i 'm a beginner in molecular dynamics. I was doing the tutorial of md group, hydration free energy of toluene : http://md.chem.rug.nl/education/Free-Energy_Course/2.hydration-fe.html i have some problems regarding the calculation of toluene in water. the thing is that in the examples files equ-10.00.mdp and data-10.00.mdp no sc-power were mentioned and doing the calculation the error files mentioned about sc-power must be >0 so i added this line sc-power=1 to those files. Analyzing the dgdl.xvg files the estimate error(err. est.) is about 5.79 for each lambda value studied while the mutation of toluene to dummy in vacuo gave really reasonable rms of about 10E-5. Combining the integration value of the plot in water and vacuo did not give me the right solvation free energy value (compare to experimental one). i assumed that this is the free calculation in water which is problematic. I tried to play with sc-power and sc-alpha but still even if those parameters seem to influence a lot on the energy no real improvement are visible. Would you have any idea what could be the problem? geraldine Helsinki university ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or s
Re: [gmx-users] (no subject)
Hi First of all: You can be quite happy, if anyone reads a "no subject" mail. sc-power seems to be set to zero in the newer version, in contrast to the old ones, where it was 1 by default. Therefore GROMACS complains. 1 is the value, you should use. I don't know the tutorial, but if you use exactly the files given there (and add sc-power = 1), you should get values, which are close to the experimental one (I guess, cause a tutorial won't make sense, if the files don't yield the desired value). Sorry, but more help is hard to give with so few information. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi all, i 'm a beginner in molecular dynamics. I was doing the tutorial of md group, hydration free energy of toluene : http://md.chem.rug.nl/education/Free-Energy_Course/2.hydration-fe.html i have some problems regarding the calculation of toluene in water. the thing is that in the examples files equ-10.00.mdp and data-10.00.mdp no sc-power were mentioned and doing the calculation the error files mentioned about sc-power must be >0 so i added this line sc-power=1 to those files. Analyzing the dgdl.xvg files the estimate error(err. est.) is about 5.79 for each lambda value studied while the mutation of toluene to dummy in vacuo gave really reasonable rms of about 10E-5. Combining the integration value of the plot in water and vacuo did not give me the right solvation free energy value (compare to experimental one). i assumed that this is the free calculation in water which is problematic. I tried to play with sc-power and sc-alpha but still even if those parameters seem to influence a lot on the energy no real improvement are visible. Would you have any idea what could be the problem? geraldine Helsinki university ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Deviations in free energies with slow growth (single and 3-step process)
David Thanks for your answer. I'm aware of that problem, but the idea was, that such a small system is very close to equilibrium on a 10ns timescale (maybe to optimistic). Actually, the thought behind it was to compare the results of the different free energy calculation methods. Now, if I assume slow growth has a systematic error of X because of non-equilibrium, I expect this error to occur more or less in the 1_step and in the 3_step calculation. However, I didn't mention, but I also did non-equilibrium tests (e.g. BAR) with this system and the deviation is exactly the same; means: BAR gives a difference of 7 kJ/mol for the ethane to methanol in 1_step hardcore and 3_step hc/sc/hc for the first and third being coulomb and the second being Lennard Jones. This actually puzzles me a bit, cause in the case of some tripeptide sidechain morphing (SER to ALA), the results of 1_step and 3_step perfectly match. I don't have to tell you, that the cycle together with the sim in gas phase gives a difference in free energy of solvation which is somewhat 15 kJ/mol away from the experiment, though. ;) For me the question arises, how to publish such "shitty" results. Do you think, 7 kJ/mol lies within the usual error of free energy calculations? If, one could never resolve reliably smaller free energy differences and the whole method won't be applicable for say drug screening or so. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ David Mobley wrote: Maik, I simulated a switching process (slow growth TI) over 10ns of ethane to methanol with hardcore slow-growth in water (365 TIP4P waters,PME) and in vacuum. The thermodynamic cycle of this calculation yields a DeltaG, which is in perfect agreement with the experiment and other calculations. Slow growth is notoriously problematic, because it only gives the true free energy in the limit that you do it infinitely slowly. Otherwise you're really measuring nonequilibrium work values, which are connected to free energies but only in an average way (see the Jarzynski relationship for a more recent discussion of this). This could be a classic example of "just because a method gives perfect agreement with experiment, you can't be sure it's giving the correct value for the force field." In other words, since force fields have their own limitations, we can't necessarily expect that when we do things right, we'll get optimal agreement with experiment. In some cases one may get better agreement with experiment by doing things *wrong* than by doing them right. i.e., suppose the correct value for the force field is actually off by 2 kJ/mol from the experimental value. If you make a protocol mistake, there's roughly a 50% chance (assuming the errors are randomly distributed!) that it will give you a value that's closer to the experimental value than your original value was. Now, when splitting this simulation into 3 steps (3x 3.2ns), where I switch the charges to zero in the first step (hardcore), morph the LJ and bonded in the second (softcore or hardcore) and switch the charges back on from zero in the third step (hardcore), all in solvent, the sum of the single contributions does NOT yield the same number as the "single-step switching". In vacuum, the work values I get from the single step process and from adding up the values from the 3-step process perfectly match. The topologies for all systems are the same (except +/- water) for the 1-step and the 3-step simulations. Now I'm a bit puzzled and can't get an idea, where this difference in the solvated system may come from. I exclude a problem due to softcore, cause I also simulated the 3-step process all hardcore... Any ideas? I'm betting your problems are largely due to the fact you're doing slow growth. Again, see the Jarzynski relationship; I especially recommend his Phys. Rev. E. paper on convergence (2001?). It's also worth noting that slow growth transformations in different directions have different convergence properties, and with slow growth (interestingly enough) particle insertion actually converges more quickly than particle deletion. So you could try reversing the direction of the transformations and see what happens. But again, slow growth isn't recommended these days -- you should probably make sure you have a very good reason for doing it and are aware of the limitations. Best, David Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel.
Re: [gmx-users] pdb2gmx: Adding non standard residues and molecular moieties
Sorry, with this question, probably no one can help you. You're probably missing a FF entry. Which FF are you actually using? Search the mailing list/Wiki for how to parametrize a molecule! Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Eddie Mende wrote: Greetings I am trying to generate a topology file, and need to add the phosphate ion in my pdb How to do this? Thanks eduardo Graduate minion some random prestigious program ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE : FEP : separating components of dgdl
> Maik, what is the power you are using for soft core ? As Berk and others suggested, sc-power = 1. regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ BON Michael wrote: ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] FEP : separating components of dgdl
Hi This warning is really strange. You could try to execute grompp with -pp to get the preprocessed topology and have a look, if the the B-parameters are included correctly. As far as I know, it should; I do it the same way. Anyway, you could also explicitly take the parameters for that dihedral from the forcefield and write them in the topology. BTW, in your case its not problematic anyway, cause they are the same :) Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ BON Michael wrote: Thanks Maik for your parameters for amber99 soft core ! Berk, you were right. The missing term is indeed the one associated to the use of constraints=all-bonds. And yes, there was a mistake in my .top file... May I ask an other question ? I still have a warning message with grompp : "WARNING 1 [file "XXX.itp", line 3451]: Some parameters for bonded interaction involving perturbed atoms are specified explicitly in state A, but not B - copying A to B" where as the line 3451 is (dihedral) : 175 177 178 187 1 nucleic_imp_10 nucleic_imp_10 nucelic_imp_10 being defined in ffamber99bon.itp. It seems to me that the state B is explicitly specified. How to get rid of this warning ? It does what I want anyway, but I want to understand what is happening. Thanks, Michaël Bon ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Deviations in free energies with slow growth (single and 3-step process)
Hi all I ran into a problem while testing some free energy methods. I simulated a switching process (slow growth TI) over 10ns of ethane to methanol with hardcore slow-growth in water (365 TIP4P waters,PME) and in vacuum. The thermodynamic cycle of this calculation yields a DeltaG, which is in perfect agreement with the experiment and other calculations. Now, when splitting this simulation into 3 steps (3x 3.2ns), where I switch the charges to zero in the first step (hardcore), morph the LJ and bonded in the second (softcore or hardcore) and switch the charges back on from zero in the third step (hardcore), all in solvent, the sum of the single contributions does NOT yield the same number as the "single-step switching". In vacuum, the work values I get from the single step process and from adding up the values from the 3-step process perfectly match. The topologies for all systems are the same (except +/- water) for the 1-step and the 3-step simulations. Now I'm a bit puzzled and can't get an idea, where this difference in the solvated system may come from. I exclude a problem due to softcore, cause I also simulated the 3-step process all hardcore... Any ideas? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] MD of DNA-protein complex AND non-protein inhibitor
To enhance Marks reply. One way to do it could be: Take the pdb-structure of your ligand and feed it to a QM-software (e.g. Gaussian). Optimize the geometry and compute the partial charges (RESP). The bonded interaction are, as usual somewhat more tricky; maybe this GAFF from amber can help you with that. If not, try to find the correct atom types and the according bonds,angles and dihedrals. All this is in fact really advanced MD stuff. Don't think you can do it by some clicking in a program. You have to read the background literature about parametrization and test your topologies in the best case against some experimental data. Good luck Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ jlenz wrote: dear gromacs users, i used gromacs calculate MD trajectories of protein and DNA covalently linked. to do so i applied the AMBER ff ports. afterwards i used a molecular docking tool to dock small non-protein ligands into potential cavities built of the DNA-protein complex. now i am facing the problem, that i again want to simulate the molecular dynamics of the most promising complexes of the protein-DNA complex and the ligand but do not know which force field to use. additionally how can i set up the parameters for the ligands? any suggestions would be of great help thanks in advance greetings joern ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Rugged dG/dlambda when turning off charges
As long as you morph pyrimidine into pyrimidine and purine into purine, everything is fine, I'd say. Morphing a pyrimidine into a purine is really problematic, cause you have to morph the whole nucleoside. Until now I didn't find a possibility to do that without perturbing all atoms of the base, which leads to a very heavy perturbation and therefore a very "spiked" dG/dl. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: Thanks Maik for your advice. I think what I'm going to do is to look at the relative binding free energy differences between the bases. Thus, I will morph the bases into one another, leaving the sugar and phosphate intact. Do you think this is a better strategy? Thanks, Bob On 1/28/08, Maik Goette <[EMAIL PROTECTED]> wrote: OK, forget my first reply and the mentioned topology splitting ;) It MAY be a problem, that you switch off two charged molecules, but I really dont know, if this is the problem. Try some totally artificial process, where you build a neutral base and use no counterion and morph the neutral base away. From my experience with DNA I can tell you, that these huge fluctuations are quite intrinsic due to the size of the perturbation. Actually, I don't have an idea, how to get rid of them. Trying to sample much longer could help to converge the system. Furthermore, using more lambda-steps could help you in getting a better total error and stuff. Again, from my experience I can tell you, that calculating free energies from letting nucleotides appear/disappear is really no fun. If you come up with a solution yourself, I would be highly interested in it. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: Thanks David, Since I'm turning off the VdW parameters as a second step, there really isn't any reason to use the soft core potentials when turning off the charges right? Thus, sc_alpha should be set to zero when turning off charges? Thanks, Bob On Jan 25, 2008 5:38 PM, David Mobley <[EMAIL PROTECTED]> wrote: It will only be smooth if you don't use soft core (i.e. sc-alpha =0 ). Best, David Mobley http://www.dillgroup.ucsf.edu/~dmobley On Jan 25, 2008 12:40 PM, Robert Johnson <[EMAIL PROTECTED]> wrote: Hello everyone, As I mentioned in a previous post, I'm trying to compute the free energy of binding of a DNA base on a carbon nanotube. My system consists of a single DNA nucleotide (base, sugar, phosphate group) on a rigid carbon nanotube in aqueous solution. A single Na+ counterion is also included for charge neutralization. I'm proceeding with this by computing the free energy associated with the following transformations: Water + Nanotube + DNA + Na+ -> Water + Nanotube + Nothing Water + DNA + Na+ -> Water + Nothing For each of these transformations I FIRST turn off the charges on the base and counterion over a set of 5 lambda values (0.0, 0.25, 0.5, 0.75, 1.0). From literature and other posts on the GMX mailing list, it seems like this small set of values should be adequate because dG/dlambda tends to be pretty smooth for discharging the molecule. Unfortunately, that doesn't seem to be the case in my system. Here is a table of the dG/dlambda values I get from running 5 ns trajectories of my system: lambda 0.0 6211.105 0.25 1055.254 0.5 1230.675 0.75 1128.359 1.0 756.2904 If you plot this you will see a large drop from lambda=0 to 0.25. Then dG/dlambda increase slightly from lambda=0.25 to 0.5 and then smoothly decreases after that. This seems like a pretty strange result. Also, it seems that something weird is going on around lambda=0. If I compute dG/dlambda for lambda=0.05, I get something around 1200-1300, which is again a very sharp decrease from the value of 6211.105 I get at lambda=0. Thus, it doesn't seem like simply adding more lambda values is going to help me. Here are the values I'm using for the free energy calculation: free_energy = yes init_lambda = 0.05 delta_lambda= 0 sc_alpha= 0.5 sc_power= 1 sc_sigma= 0.3 Also, here is an excerpt from my topology file: [ atoms ] 1 P 1 DG P 1 1.1659 30.9700 P 0. 30.9700 2 O 1 DG O1P 1 -0.7761 16. O
Re: [gmx-users] RE : FEP : separating components of dgdl
I think, there are some "best" parameters :) Ich tested them with some smaller systems and found, that sigma=0.3 and alpha=0.25 seem to perform quite well. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ BON Michael wrote: Hi, You were right for the bonds, I forgot that I was using constraints = all-bonds. Could the missing term be the soft core then ? Or is it included in VdW ? Anyway, I noticed that this problem of hidden extra term happens when I modify something else than a hydrogen. Does it make sense ? For example, I did N->DUM with all the parameters kept the same : every components of dVdl are 0 (VdW, Coulomb, angle, proper dihedral, Ryck., LJ 1-4, position restraint, disp. corr. ), but dVdl/dlambda is -6. Any idea ? Other question : is there some information available about the "best" settings of soft core parameters with amber99 ? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Rugged dG/dlambda when turning off charges
OK, forget my first reply and the mentioned topology splitting ;) It MAY be a problem, that you switch off two charged molecules, but I really dont know, if this is the problem. Try some totally artificial process, where you build a neutral base and use no counterion and morph the neutral base away. From my experience with DNA I can tell you, that these huge fluctuations are quite intrinsic due to the size of the perturbation. Actually, I don't have an idea, how to get rid of them. Trying to sample much longer could help to converge the system. Furthermore, using more lambda-steps could help you in getting a better total error and stuff. Again, from my experience I can tell you, that calculating free energies from letting nucleotides appear/disappear is really no fun. If you come up with a solution yourself, I would be highly interested in it. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: Thanks David, Since I'm turning off the VdW parameters as a second step, there really isn't any reason to use the soft core potentials when turning off the charges right? Thus, sc_alpha should be set to zero when turning off charges? Thanks, Bob On Jan 25, 2008 5:38 PM, David Mobley <[EMAIL PROTECTED]> wrote: It will only be smooth if you don't use soft core (i.e. sc-alpha =0 ). Best, David Mobley http://www.dillgroup.ucsf.edu/~dmobley On Jan 25, 2008 12:40 PM, Robert Johnson <[EMAIL PROTECTED]> wrote: Hello everyone, As I mentioned in a previous post, I'm trying to compute the free energy of binding of a DNA base on a carbon nanotube. My system consists of a single DNA nucleotide (base, sugar, phosphate group) on a rigid carbon nanotube in aqueous solution. A single Na+ counterion is also included for charge neutralization. I'm proceeding with this by computing the free energy associated with the following transformations: Water + Nanotube + DNA + Na+ -> Water + Nanotube + Nothing Water + DNA + Na+ -> Water + Nothing For each of these transformations I FIRST turn off the charges on the base and counterion over a set of 5 lambda values (0.0, 0.25, 0.5, 0.75, 1.0). From literature and other posts on the GMX mailing list, it seems like this small set of values should be adequate because dG/dlambda tends to be pretty smooth for discharging the molecule. Unfortunately, that doesn't seem to be the case in my system. Here is a table of the dG/dlambda values I get from running 5 ns trajectories of my system: lambda 0.0 6211.105 0.25 1055.254 0.5 1230.675 0.75 1128.359 1.0 756.2904 If you plot this you will see a large drop from lambda=0 to 0.25. Then dG/dlambda increase slightly from lambda=0.25 to 0.5 and then smoothly decreases after that. This seems like a pretty strange result. Also, it seems that something weird is going on around lambda=0. If I compute dG/dlambda for lambda=0.05, I get something around 1200-1300, which is again a very sharp decrease from the value of 6211.105 I get at lambda=0. Thus, it doesn't seem like simply adding more lambda values is going to help me. Here are the values I'm using for the free energy calculation: free_energy = yes init_lambda = 0.05 delta_lambda= 0 sc_alpha= 0.5 sc_power= 1 sc_sigma= 0.3 Also, here is an excerpt from my topology file: [ atoms ] 1 P 1 DG P 1 1.1659 30.9700 P 0. 30.9700 2 O 1 DG O1P 1 -0.7761 16. O 0. 16. 3 O 1 DG O2P 1 -0.7761 16. O 0. 16. I'm not perturbing any of the bonding interactions or VdW parameters - I'm just turning off all charges on the molecule. Does anyone have any ideas or suggestions about how this can be improved? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or
Re: [gmx-users] Rugged dG/dlambda when turning off charges
The point is: You want to do a severe perturbation. May I inform you, that I tried morphing base pairs for 3 years and now quitted? ;) Anyway, if you have such a strong perturbation, you should think about a different setup, like softcore for vdw and harcore for qq. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: Hello everyone, As I mentioned in a previous post, I'm trying to compute the free energy of binding of a DNA base on a carbon nanotube. My system consists of a single DNA nucleotide (base, sugar, phosphate group) on a rigid carbon nanotube in aqueous solution. A single Na+ counterion is also included for charge neutralization. I'm proceeding with this by computing the free energy associated with the following transformations: Water + Nanotube + DNA + Na+ -> Water + Nanotube + Nothing Water + DNA + Na+ -> Water + Nothing For each of these transformations I FIRST turn off the charges on the base and counterion over a set of 5 lambda values (0.0, 0.25, 0.5, 0.75, 1.0). From literature and other posts on the GMX mailing list, it seems like this small set of values should be adequate because dG/dlambda tends to be pretty smooth for discharging the molecule. Unfortunately, that doesn't seem to be the case in my system. Here is a table of the dG/dlambda values I get from running 5 ns trajectories of my system: lambda 0.0 6211.105 0.25 1055.254 0.5 1230.675 0.75 1128.359 1.0 756.2904 If you plot this you will see a large drop from lambda=0 to 0.25. Then dG/dlambda increase slightly from lambda=0.25 to 0.5 and then smoothly decreases after that. This seems like a pretty strange result. Also, it seems that something weird is going on around lambda=0. If I compute dG/dlambda for lambda=0.05, I get something around 1200-1300, which is again a very sharp decrease from the value of 6211.105 I get at lambda=0. Thus, it doesn't seem like simply adding more lambda values is going to help me. Here are the values I'm using for the free energy calculation: free_energy = yes init_lambda = 0.05 delta_lambda= 0 sc_alpha= 0.5 sc_power= 1 sc_sigma= 0.3 Also, here is an excerpt from my topology file: [ atoms ] 1 P 1 DG P 1 1.1659 30.9700 P 0. 30.9700 2 O 1 DG O1P 1 -0.7761 16. O 0. 16. 3 O 1 DG O2P 1 -0.7761 16. O 0. 16. I'm not perturbing any of the bonding interactions or VdW parameters - I'm just turning off all charges on the molecule. Does anyone have any ideas or suggestions about how this can be improved? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Virtual site and constraints
Virutal particles should not have any mass. Its, e.g. for placing a delocalized charge (as in TIP4P) somewhere. How about carefully reading the warnings and try to do, what they suggest? How about this?: > 5 opls_966 1FMT D 112.0110.0 Now you have a charge there and no mass. Thats, how virtual sites work. If you want to use a "free energy dummy", you may have to use a different approach. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Нилов Дмитрий wrote: I`ve tried to name it like atom (instead of "dummy mass") in this way: 1)enter new atom type in "ffoplsaa.atp": opls_966 12.01100 ; Virtual site in formate 2)enter description of new atom type in "ffoplsaanb.itp": ; name bond_type masscharge ptype sigma epsilon opls_966 DF 0 12.011 0. D 0.00e+00 0.00e+00 (also I`ve tried to use "A" instead of "D" in ptype column) 3)correct my topology: [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_279 1FMT H 1 0.22 1.008 2 opls_271 1FMT C 1 0.58 0.000 3 opls_272 1FMT O1 1 -0.915.9994 4 opls_272 1FMT O2 1 -0.915.9994 5 opls_966 1FMT D 10.0 12.011 [ constraints ] ; aiaj functc0 1 3 20.19850 1 4 20.19850 3 4 20.22400 [ virtual_sites3 ] ; Dummy from funct a b 2 1 3 4 1 0.345 0.345 5 1 3 4 1 0.345 0.345 But it does not work because grompp runs with error "virtual site D (Res FMT-1) has non-zero mass 12.011". I suppose, that only "dummy masses"(particles named like "M*") could have mass. Could you help me, please? Nilov Dmitri -Original Message- Нилов Дмитрий wrote: OK, could I add "dummy mass" that has coordinates and mass such as carbon to keep right moment of inertia? I mean something like this: [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_279 1FMT H 1 0.22 1.008 2 opls_271 1FMT C 1 0.58 0.000 3 opls_272 1FMT O1 1 -0.915.9994 4 opls_272 1FMT O2 1 -0.915.9994 5 MW 1FMT D 10.0 12.011 Should I use some constraints for "dummy mass" to define its position in simulation? And can I get "dummy mass" type from ffoplaa.atp or its better to add the new one? Have you tried naming it an atom instead of a virtual site? I`m sorry, I`ve read manual and corresponding article but I have not find irrefragable answer for my questions. Thanks Nilov Dmitri Нилов Дмитрий wrote: Thank you very much, but in what way can I define the carbon like massless when it treated as a virtual site(type 3) in formate molecule? You can define it as zero, but take care to get the right moment of inertia (by defining further virtual sites). Grompp runs with error when carbon has mass: converting bonded parameters... # CONNBONDS: 3 # CONSTR: 3 # VSITE3: 1 Setting particle type to V for virtual sites ERROR 2 [file "fmt.top", line 82]: virtual site C (Res FMT-1) has non-zero mass 12.011 - -Original Message- Нилов Дмитрий wrote: Hello! I would like to involve formate molecule (HCOO-)in my dynamics, but I have the problem when I use virtual site (type 3fd)for it. When I run grompp for single formate molecule, it`s ok. But after solvating in bath of solvent (tip3p) grompp runs with error: In this case you would be best off defining three constraints from H O1 H O2 O1 O2 and define the carbon as a virtual site defined by the plane (check TIP4P topology). -- David van der Spoel, Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archiv
Re: [gmx-users] FEP trajectory errors
Do really all atoms "freeze". So also the atoms, which are not perturbed? Can you post your mdp-file? Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: The distortion was occuring because my position restraint potential was too weak. Increasing the force constant keeps the base in the right conformation. I believe my topology is correct, but it seems that turning off the VdW parameters causes the base to distort. I will look into this more. Also, even with sc_alpha=0.5, I'm still experiencing this weird "freezing" when lambda=1.0. The trajectory proceeds normally for about 2.1 ns, then all of a sudden all motion freezes and the atoms simply vibrate about their "equilibrium positions". Any other ideas what might cause this? Thanks, Bob On Jan 21, 2008 3:39 AM, Maik Goette <[EMAIL PROTECTED]> wrote: Robert A value for alpha of 0.5 should work, although I tested some different alphas with different test systems and I have to say, that a proper value can be between 0.2 and 0.7 depending on the system itself. The distortion, you describe is really strange. I calculated DNA and single bases a lot and never saw something like that. Even a fully "dummy-base" is stable, if your topology is correct. The bonded terms are sufficient to keep it in the right conformation. Are you sure, your position restrains in the topology are used with the correct structure file? Maybe, I should also mention, that, especially with such large perturbations as a full DNA-base, you should split your topology into 2, where you switch off the QQ hardcore and the VdW softcore in two steps. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: Thank you David and Maik for your detailed replies. Yes, I am trying to obtain an absolute free energy of binding. My thermodynamic cycle is: NT+DNA(adsorbed) -> NT+ DNA(desorbed) (obviously this is not the one that I'm obtaining with the alchemic method) Thus, the one I'm using in the simulation is: Water + NT + DNA(adsorbed) -> Water + NT + nothing (DNA dissapears) Water + DNA -> Water + nothing Any suggestions about this? I will check out your recent publications. I believe my topology is properly formatted. I wasn't expecting the large distortions because I was using position restraints. Thus, I was expecting the base to remain in about the same geometry. Perhaps I will increase the force constant for the restraining potential. I am going to repeat some of these computations using sc_alpha=0.5. Thanks for your help. Bob On Jan 17, 2008 2:24 PM, David Mobley <[EMAIL PROTECTED]> wrote: Robert, I'm computing the free energy of binding of a DNA base on a carbon nanotube. I think it's a pretty simple calculation and I'm proceeding in a very standard way. This is what I'm doing: An absolute free energy? This isn't necessarily straightforward -- there are a lot of wrinkles. Some of my recent work has some discussions if this if it's helpful. I have the optimal orientation of the base on the nanotube. I'm constraining the positions of the base atoms with a soft harmonic potential. OK, that's a good idea for standard state reasons (see the 2003 Boresch paper) among other things. I then am running two different FEP calculations: one where I turn off the charges on the base atoms and a second where I then turn off all the lennard-jones parameters for the base atoms. For each of these I use the following: delta_lambda = 0 sc_alpha = 0.7 sc_power = 1 sc_sigma = 0.3 I run a series of trajectories at constant lambda values from 0 to 1. OK. I have some information posted on what I think the best settings are for these on alchemistry.org, especially at http://www.alchemistry.org/wiki/index.php/Best_Practices. It is still in progress but may be somewhat helpful. I doubt this is the source of your problems though, although I prefer a sc_alpha = 0.5 which may improve the situation somewhat. However, I notice some problems with the trajectories when I turn off the LJ parameters. As lambda is varied from 0 to 1, it seems that the position restraints no longer are being applied. Additionally, the DNA base geometry starts to become severely distorted at lambda values greater than about 0.6. This happens despite the fact that I am not perturbing the
Re: [gmx-users] source code change
You're welcome... Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ avinash kumar wrote: To Maik Goette, Thank you for your reply. Avinash Kumar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] a problem,Thank you
This has been discussed several times...
Search the mailing list archive.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
[EMAIL PROTECTED] wrote:
I use ffamber94 in gromacs,and I also use spc water model
However,I get wrong information when I am running grompp
Fatal error:
[ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]:
Atom index (1) in settles out of bounds (1-0)
I don't know how to solve it ,please help me
Thank you!!!
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Today's Topics:
1. source code change (avinash kumar)
2. Re: source code change (David van der Spoel)
3. Re: GMX CPMD K+ ion problem (ggroenh)
4. Re: problem regarding grompp ([EMAIL PROTECTED])
5. Re: problem regarding grompp (Mark Abraham)
--
Message: 1
Date: Sat, 19 Jan 2008 21:01:01 +0530
From: "avinash kumar" <[EMAIL PROTECTED]>
Subject: [gmx-users] source code change
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset=UTF-8
Hello all,
Thank you Xavier for your reply. I will explain why I want to change
the source code. I have to implement a modified Lennard Jones
potential,
â§
âª
⨠4 *epsilon{( _Ï_ )^12 â (_Ï_ )^6} â VLJ (rc ), r â¤
rc ,
r r
V (r) =
âª
â© 0, r > rc ,
The original Lennard Jones potential has no -VLJ(rc) term. This means
I want to subtract some constant from the Lennard Jones potential
which the GROMACS will calculate. Please tell me where in the GROMACS
source code should I make a change so that it will be implemented.
Afterwards will I need to compile it again?
Thanks in advance,
Avinash
--
Message: 2
Date: Sat, 19 Jan 2008 16:34:18 +0100
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] source code change
To: Discussion list for GROMACS users
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
avinash kumar wrote:
> Hello all,
>
> Thank you Xavier for your reply. I will explain why I want to change
> the source code. I have to implement a modified Lennard Jones
> potential,
>
> ?
> ?
> ? 4 *epsilon{( _?_ )^12 - (_?_ )^6} - VLJ (rc ), r ? rc ,
> r r
>
> V (r) =
> ?
> ? 0, r > rc ,
>
> The original Lennard Jones potential has no -VLJ(rc) term. This means
> I want to subtract some constant from the Lennard Jones potential
> which the GROMACS will calculate. Please tell me where in the GROMACS
> source code should I make a change so that it will be implemented.
> Afterwards will I need to compile it again?
>
Why not use one of the built-in shift potentials? This change will have
no effect on the dynamics and only add a constant to the overall energy.
Another alternative is to use a tabulated potential.
> Thanks in advance,
> Avinash
>
>
>
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, De
Re: [gmx-users] source code change
Avinash > Afterwards will I need to compile it again? Don't want to be mean, but are you sure, after such a question, you can actually write and understand C-code? Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ avinash kumar wrote: ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] FEP trajectory errors
Robert A value for alpha of 0.5 should work, although I tested some different alphas with different test systems and I have to say, that a proper value can be between 0.2 and 0.7 depending on the system itself. The distortion, you describe is really strange. I calculated DNA and single bases a lot and never saw something like that. Even a fully "dummy-base" is stable, if your topology is correct. The bonded terms are sufficient to keep it in the right conformation. Are you sure, your position restrains in the topology are used with the correct structure file? Maybe, I should also mention, that, especially with such large perturbations as a full DNA-base, you should split your topology into 2, where you switch off the QQ hardcore and the VdW softcore in two steps. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: Thank you David and Maik for your detailed replies. Yes, I am trying to obtain an absolute free energy of binding. My thermodynamic cycle is: NT+DNA(adsorbed) -> NT+ DNA(desorbed) (obviously this is not the one that I'm obtaining with the alchemic method) Thus, the one I'm using in the simulation is: Water + NT + DNA(adsorbed) -> Water + NT + nothing (DNA dissapears) Water + DNA -> Water + nothing Any suggestions about this? I will check out your recent publications. I believe my topology is properly formatted. I wasn't expecting the large distortions because I was using position restraints. Thus, I was expecting the base to remain in about the same geometry. Perhaps I will increase the force constant for the restraining potential. I am going to repeat some of these computations using sc_alpha=0.5. Thanks for your help. Bob On Jan 17, 2008 2:24 PM, David Mobley <[EMAIL PROTECTED]> wrote: Robert, I'm computing the free energy of binding of a DNA base on a carbon nanotube. I think it's a pretty simple calculation and I'm proceeding in a very standard way. This is what I'm doing: An absolute free energy? This isn't necessarily straightforward -- there are a lot of wrinkles. Some of my recent work has some discussions if this if it's helpful. I have the optimal orientation of the base on the nanotube. I'm constraining the positions of the base atoms with a soft harmonic potential. OK, that's a good idea for standard state reasons (see the 2003 Boresch paper) among other things. I then am running two different FEP calculations: one where I turn off the charges on the base atoms and a second where I then turn off all the lennard-jones parameters for the base atoms. For each of these I use the following: delta_lambda = 0 sc_alpha = 0.7 sc_power = 1 sc_sigma = 0.3 I run a series of trajectories at constant lambda values from 0 to 1. OK. I have some information posted on what I think the best settings are for these on alchemistry.org, especially at http://www.alchemistry.org/wiki/index.php/Best_Practices. It is still in progress but may be somewhat helpful. I doubt this is the source of your problems though, although I prefer a sc_alpha = 0.5 which may improve the situation somewhat. However, I notice some problems with the trajectories when I turn off the LJ parameters. As lambda is varied from 0 to 1, it seems that the position restraints no longer are being applied. Additionally, the DNA base geometry starts to become severely distorted at lambda values greater than about 0.6. This happens despite the fact that I am not perturbing the internal bonded interactions of the base. Here is a sample of my topology (included just the first line of each section): Hm, on the position restraints, depending on your version of gromacs you may need to additionally specifiy the B state position restraints, else these may be assumed to be zero. I believe you can do this by adding additional columns in your posre.itp that give the B state parameters. In terms of distortion, it's not clear to me why you think the molecule should *not* be distorted once you turn off the LJ interactions (which includes internal LJ interactions). The bonded parameters (especially torsions) are of course derived after LJ parameters are already fitted, in most cases, so they only can be relied on to give meaningful conformations when the LJ interactions are on. The beauty of the thermodynamic cycle approach, though, is that you can (at least in principle) get correct binding free energies even if your molecule of interest samples wacky, artificial conformations when it's noninteracting. Also, I am experiencing additional problems when lambda=1. After about 2ns, all the motion in the system begins to
Re: [gmx-users] How to remove H atom from residue in gro file?
Hi First of all, I think its dangerous to perform MD simulations without any knowledge about the details of MD. So the first suggestion is: Inform yourself (by reading the manual) about MD and GROMACS. Using a black box is, maybe, often done, but surely not the best way to go. Before starting a simulation with non-standard residues I'd suggest to start some tutorial-simulations with "normal" proteins to improve your knowledge. To solve your problem the easiest (and hopefully the best) way, I would suggest to use the amberFF port and then build your phosphorylated residues according to these parameters: N Homeyer, AHC Horn, H Lanig, H Sticht - Journal of Molecular Modeling, 2006 This is for sure some work and you need an understanding of how GROMACS makes use of residue parameters and stuff, but its IMHO the best way to produce reasonable results. regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Nelson Cotrim wrote: Hi gmx users, I am rather new to MD, Linux environment and almost everything related to it. I am a geneticist working on mutations, so please, keep it simple :) This may be trivial and there may be an answer on the list already, but I do not even know how to search for it - the way I tried did not return anything useful. I am analysing a mutation in a binding domain of a protein, and the ligand is phosporylated (a SER). I tried to use ff43a1p but kept getting errors in the FF files (hdb, rtp, etc), so instead I am used PRODRG to parametrize the PO4 (PO3+OG), changed the SEP to SER in the PDB file and then edited the .gro and .top files adding the data for the PO3. Evertyhting works great know, with the exception of the HG that pdb2gmx adds when converting the .pdb into the .gro. This HG is in the place that should be taken by the PO3, but I do not know how to remove it. Which values will I have to correct in the .top, if any? Should I just remove the line with all the parameters and just correct the subsequent atom numbers? Is there an easier and foolpŕoof method to do this (it is easy to mistype the numbers this way)? Many thanks, Nelson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] free energy calculation
I bet, this topic has been discussed on the list multiple times before. Numerical Integration is the keyword here and be aware of the problems in calculating the total error from the single errors (look into Shirts papers). I suggest to inform yourself intensively about free energy calculation methods, their pros and cons in general. Using a tutorial is not the only thing to do, to compute meaningful free energies. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Li Qiang wrote: Dear all, Can anybody tell me how to calculate the free energy difference after running simulation with lamda(0, 0.1,...1)? I am following the tutorial on wiki, but i have no idea about the details to do the "data analysis". any software can do it? and any reference for the instruction? I am new here. thanks a lot Qiang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] FEP trajectory errors
Robert I think, I cant help you too much, cause your problem involves too many sources of errors. Your topology (if continued that way) seems to be ok. Your TI-params seem to be ok, too. First, make clear: Do you use Position RESTRAINTS or (distance) CONSTRAINTS. There is a fundamental difference. Second you should be aware of how to get out the restraint/constraint term from your free energy, to get a correct one. Don't ask me how, I don't know ;) Second, I suppose, your restraints/constraints are wrong somehow. Please give some info about the restraints/constraints and the mdp-entries, you use. I'm really wondering about the distortion of your base, cause this must not happen if you perturb the bonded terms the way, you describe. Be aware, that, if you position restraint with e.g. posre.itp, B-parameters should be available there, too. I don't really know, if the A-parameters in the posre-file will be copied to B, too. Test that with a gmxdump. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: Hello everyone, I'm computing the free energy of binding of a DNA base on a carbon nanotube. I think it's a pretty simple calculation and I'm proceeding in a very standard way. This is what I'm doing: I have the optimal orientation of the base on the nanotube. I'm constraining the positions of the base atoms with a soft harmonic potential. I then am running two different FEP calculations: one where I turn off the charges on the base atoms and a second where I then turn off all the lennard-jones parameters for the base atoms. For each of these I use the following: delta_lambda = 0 sc_alpha = 0.7 sc_power = 1 sc_sigma = 0.3 I run a series of trajectories at constant lambda values from 0 to 1. However, I notice some problems with the trajectories when I turn off the LJ parameters. As lambda is varied from 0 to 1, it seems that the position restraints no longer are being applied. Additionally, the DNA base geometry starts to become severely distorted at lambda values greater than about 0.6. This happens despite the fact that I am not perturbing the internal bonded interactions of the base. Here is a sample of my topology (included just the first line of each section): [ moleculetype ] ; Namenrexcl dg-disappear 3 [ atoms ] 1 P 1 DG P 1 1.1659 30.9700 DUM 0. 30.9700 ... [ bonds ] 1 2 1 0.1480 439320. 0.1480 439320. ... [ angles ] 1 4 5 1 120.5001836.8000 120.5001836.8000 ... [ dihedrals ] 1 4 5 8 1 0. 1.6039 3 0. 1.6039 3 ... [ position_restraints ] 1 1 100 100 100 100 100 100 ... So you can see that I am not perturbing the bonded interactions as I have just copied the same values from topology A. Also, I am experiencing additional problems when lambda=1. After about 2ns, all the motion in the system begins to freeze and all the atoms simply vibrate about a fixed position. Soon after that the simulation crashes. Can anyone comment on what's going on here? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral with parameters set to zero
No Holland-Speek here! ;) Anyway, you maybe right...:) Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ van Bemmelen wrote: Hmmm, thanks. An obvious solution, but I had not yet thought of that myself. Well, you know what they say: Een dag niets geleerd is een dag niet geleefd! ;-) Date: Thu, 10 Jan 2008 19:27:38 +0100 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Dihedral with parameters set to zero To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed van Bemmelen wrote: OK. Now I'm confused. What did you mean by the second part? Of course, when doing FEP with the B state different, you would gradually introduce a dihedral as lambda increases. But that would still mean that setting all dihedral parameters to 0 for the A state would be exactly equivalent to having no dihedral at all, only for the simulation at lambda=0.0. Right? Or did you mean something else? Thanks, Jeroen P.S. Actually, in such a setup one would probably run into trouble anyway because according to the manual the multipliciy cannot be perturbed. But let's ignore that for now. but that can be solved by defining two dihedrals with different mult and turn off one and turn on the other. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.
Chris
This is, what I usually do, too.
Still you need the parameters for your ligand from somewhere ;)
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Chris Neale wrote:
When actually building the topology I find it easiest to create the
residues in the relevant .rtp and allow pdb2gmx to build the topology
for you. However, all this does is correctly connect everything and put
your parameters where they should be. All previous comments (in this
thread and the hundreds of other threads on this topic) still apply
about how to come up with the parameters... read the original papers and
reproduce their methodology.
Chris.
Dear users,
I am working with PTP1B protein. Recently I tried to
run it in gromacs along with an inhibitor
{[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN-
2-YL]-DIFLUORO-METHYL}-PHOSPHONIC ACID[FNP in short]. The problem
is that gromacs does not recognize FNP and hence I am not able to
generate a topology file of it using pdb2gmx. I tried using the The
Dundee PRODRG server to generate the topology file with the pdb file
as the input. The problem is that it does generate the topology file
but without any hydrogens. Even the polar hydrogens information is
not available inspite of it being a part of my input pdb file. Thus I
am not able to use FNP with the polar hydrogens for my runs.
If anyone has faced similar problems please do help if you can.
Thanking you,
Cheers.
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Re: [gmx-users] energy perturbation
Hi If I'm not totally wrong, a howto setup a free energy perturbation topology is written in the manual. Additionally David and others brought up several links to tutorials here in the mailing list. So simply use the search function and read the manual. A perturbed atom entry for OPLSAA ( and in fact for all others) looks like this: #ID TypeA Resn Resid Atom hargegr. ChargeA Mass A Type B Charge B Mass B 12 opls_224B 2TRP CA 3 0.14 12.011 opls_223B 0.08 12.011 A general tip: Before proceeding, inform yourself about the different free energy calculation methods and how they are used in GROMACS. Especially have a look into "softcore" and be aware of using it JUST for vdw morphing... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Farzad Molani wrote: Hi Mark I read the manual and I used umabrella sampling and I got a curve for pmf but now I want pmf by energy perturbation that I want to sure about my curve that I got by umbrella sampling. my question is about .itp file and how do I create. thank you very much. Never miss a thing. Make Yahoo your homepage. <http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs> ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How can I add ffG43a1p force field to gromacs software?
Hi Try the -ff option of pdb2gmx, if you're not able to get it working. This less complicated. pdb2gmx -f pdb.pdb -ff ffG43a1 Should work Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Mitra Kheirabadi wrote: Dear Dr.Periole I add ffG43a1p to FF.dat/ top and changed 11 to 12 on this file but sorry again I did not appear. please help me. Respectfully */Mitra Kheirabadi <[EMAIL PROTECTED]>/* wrote: Dear Periola I appreciate your kindly help. Respectfully */Xavier Periole <[EMAIL PROTECTED]>/* wrote: On Tue, 8 Jan 2008 06:35:28 -0800 (PST) Mitra Kheirabadi wrote: > Dear Dr. Smith > > I want to run a virus phosphorylated protein by gromacs. Furtunatly, you >construct related force field by ffG43A1p name. I copied this force field to >top. file gromacs but when I constructed pdbgmx, there is no any ffG43a1p to >select. Could you help me? > I be so grateful to receive any information about it. you must modify the file top/FF.dat and include the new force field. XAvier - XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Never miss a thing. Make Yahoo your homepage. <http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs> ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Looking for last minute shopping deals? Find them fast with Yahoo! Search. <http://us.rd.yahoo.com/evt=51734/*http://tools.search.yahoo.com/newsearch/category.php?category=shopping> ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology treatment in free energy calculations -possible bug
Berk Thanks for the clarification. I was aware of A-values copied to B-values, when no B-values in the FF exist, but actually this was new to me. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Berk Hess wrote: This behavior is itentional. But it can indeed be confusing. Therefore in Gromacs 4.0 a warning will be generated (and I have added a table in the manual that explains all the possible combinations). If you explicitly define parameters for the A-state, I don't see why you would want the B-parameters to be looked up based on atom-type. You would only want that when the A-state parameters are also determined by the atom type. Berk. From: Maik Goette <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: GMX-mailinglist Subject: [gmx-users] topology treatment in free energy calculations -possible bug Date: Fri, 04 Jan 2008 15:15:57 +0100 Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] topology treatment in free energy calculations - possible bug_2nd
Hi once more It just came to my mind, that the behaviour, I described in the first mail will be quite dangerous, whenever #define statements are in the topology, cause this would lead to the insertion of the FF-values in the topology, when preprocessing, and then be copied into the B-state afterwards, even if the values are crap for the B-state... Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] topology treatment in free energy calculations - possible bug
Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-state): Original topology entry: 101214 1 Manually edited entry (with the correct ff-term): 101214 1 109.700 669.440 Now, a dump from the tpr-files yields the following: Original: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02, ctB= 2.92880e+02 Edited: functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 Now, what obviously happens is, that GROMACS searches the entries of the angle in the FF for both states and uses them in the case of the original topology. If one puts a manual entry into the topology for the A-state though, the B-state is simply copied, instead of searched by GROMACS. This, IMHO, is quite inconvenient. Is this a bug or a feature? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ATP, GTP and REX
Hi You can use the AMBER ports for 3.3.2, I'd say. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Fenwick wrote: Hi, I would like to make some unrestrained simulations of ATP and GTP binding proteins and wondered if there were any topology files floating about for OPLSAA or the GROMOS96.1 forcefields for these two ligands? I understand that the gmx forcefields have been deprecated and that I should use one of the newer ones, however there are not that many ligand topology files about. I am just starting out, so any suggestions would be welcome. The systems are approximately 300 residues in size and I am interested in the stability and rms fluctuations of the systems. A secondary question is that of the AMBER forcefields, I am using the 3.3.2 version, however the amber files state specifically to use the port for the relevant version, one of which is missing for 3.3.2. Is it safe to use the 3.3.1 amber ff port with version 3.3.2 of GROMACS? Finally, if anyone can point me in the direction of a small test project that does some simple replica exchange, with some instructions as to how to get it to run, I would be very grateful. Bryn ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] free energy calculations in charged systems
Hi Cant' give you a sound answer, but from what I heard from talking to people in the field, PME can't handle that properly. Maybe Cut-Off/Reaction-Field should be the long-range treatment of choice. Still, I don't know, if there may occur problems with that. Maybe David (both) or Berk have some more sound comments on that. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Argyrios Karatrantos wrote: Hi all, i am working in polyelectrolyte solutions, and i would like to calculate the free energy for the polyectrolyte system (charged) to change to a neutral (non-charged) system. The question is if it feasible to use the PME electrostatics in gromacs for the above free-energy calculation. thanks Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to specify .mdp file for position restrained simulation?
Hi Use the following term in your mdp: define = -DPOSRES Now, everything is true, depending on the question you ask and the point you're standing... What you may mean is the following: POSRES-Sims are mostly (not always) used for equilibrating the solvent around the protein. These simulations are in general quite short, because relaxation of water happens quite fast. In this case a Posres-Sim is much shorter (say 200ps or so) than a "real" run (usually in the range of ns). Please be aware, that there is also a parameter file for position-restraints (e.g. posre.itp), which, if automatically generated by pdb2gmx contains the positions of all heavy atoms with a force constant for x,y,z. And now a suggestion. Please, before starting MD inform yourself about: a. The theoretical aspects of molecular dynamics b. The program you are using (i.e. the manual) The probability of getting good results and no crap increases dramatically with following the two points above... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Peggy Yao wrote: Hi, How to specify the .mdp file in order to run position restrained simulation? From the examples I found on the internet, it seems that the only difference between the .mdp file for position restrained simulation and the one for actual MD simulation is the simulation time -- the position restrained simulation is much shorter. Is this observation true in general? If yes, usually, how long is enough for the position restrained simulation? If not, how to specify the .mdp file for position restrained simulation then? Thanks a lot! Peggy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Minor Bug in latest stable release update
Hi I found a missing entry in include/pme.h. Could be connected to the free energy/PME problems, Berk recently solved. In the declaration of spread_on_grid, there's a variable in the function missing. This is how it looks: extern void spread_on_grid(FILE *logfile, t_fftgrid *grid, int homenr, int pme_order, rvec x[], real charge[], matrix box, bool bGatherOnly,bool bHaveSplines); This is how it should: extern void spread_on_grid(FILE *logfile, t_fftgrid *grid, int homenr, int pme_order,rvec x[], real charge[],matrix box, bool bGatherOnly, bool bFreeEnergy, bool bHaveSplines); Leads to a break while compiling GROMACS Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ffamber updates
Hi Eric Thanks for doing that great job concerning the amberFF for GROMACS. I recently came across this paper: http://www.biophysj.org/cgi/content/abstract/92/11/3817?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=92&firstpage=3817&resourcetype=HWCIT There Perez et al refined new alpha/gamma angles for nucleic acids. They claim, that these dihedrals in the original amber99 lead to irreversible transitions, which have an influence on the correct conformation of NA-strands. I thought about including them in the amber99-GROMACS port, but maybe it's better if you do, because you have more experience in building the amber-ports. What do you think? I didn't read the paper according to your 99sb-port yet. Do you think it makes sense to switch from the amber99 to amber99sb? Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Eric J. Sorin wrote: Hi GROMACS users, We've updated our ffamber ports to include the AMBER-99SB force field. Please visit the new website for information and downloads: http://chemistry.csulb.edu/ffamber/. Eric ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs result
Right, but I can just warn anyone. Trying to use TI on a docked structure is insanity... The docked structure is an approximation in its best case (more likely its simply crap). Applying a free energy calculation towards such a structure will give you everything...but sure not the the correct free energy of bindingexcept you are very luckyIF you are that lucky, play lottery instead and enjoy life ;) In fact it's (citating Mark) another expensive random number generator... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Mark Abraham wrote: mahbubeh zarrabi wrote: Dear all I have 3 complexes of docking.(one receptor with 3 different ligands).I studied MD of 3 complexes in 15 ns by gromacs.how can i compare binding energy and affinity of 3 ligands with receptor.(how can i analysis gromacs result) Shouldn't you have asked this question before designing your simulations? :-) You can't measure binding affinity without taking a difference between "before" and "after", which you don't seem to have. You probably need to look at literature on thermodynamic integration, or some such. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: "Impulsive" motion resulting from AFM pulling
Hmm.looks really strange... What do you see in a visualization of the trajectory? Do you see the whole tube hopping? Or does it somehow stretch and shrink? To me, the wells look somehow harmonic, what may be related to the spring (constant). Maybe, try a different spring constant for testing. Is the position you plot the com or the pull group? Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote: Can anyone recommend a remedy/explanation for this? Thanks, Bob On 9/19/07, Robert Johnson <[EMAIL PROTECTED]> wrote: Hello everyone, Eventually I want to pull a carbon nanotube through water at a constant rate. Before I get to this, I'm pulling a nanotube in vacuum just to make sure I'm using the pull code correctly. My system consists of a carbon nanotube aligned along the z axis and a single dummy atom fixed on the z axis. Here is my pull.ppa file: runtype = afm ngroups = 1 group_1 = nanotube pulldim = Y N N reference_group = dummy reftype = com afm_rate1 = 0.1 afm_dir1 = 1 0 0 afm_k1 = 10 afm_init1 = 2.00 2.00 4.042 Here, the coordinates for afm_init1 is the initial center of mass of the nanotube (thus, the system should start out with zero applied force). Applying this pulling force results in the nanotube undergoing a complicated oscillation as it moves along the +x direction. A graph of the nanotube position as a function of time is shown here: http://dept.physics.upenn.edu/~robertjo/gmx/nt-position.jpg What is causing oscillations of this type? I was expecting the nanotube to move at a constant rate. Does this have anything to do with the fact that I'm pulling the nanotube in vacuum? Perhaps in aqueous solution, the solvent will damp these types of oscillations. Any ideas as to how to remove this? Thanks, Bob ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Help! A dummy atom definition problem!
The problem actually is, that you mixed up a dummy atom with a virtual site, I guess. Virtual sites are not allowed to have a mass, as the error message claims. Also, a proper hydrogen should have a mass. If you want a hydrogen to appear, you have to place a particle in A-state which has no non-bonded interaction, i.e. LJ & QQ interactions should be zero. If you want to prevent it from flying away, you should put bonded terms to the particle. In the B-state, the QQ and LJ should be there (whereas the LJ interaction for a hydrogen is 0 anyway). 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 opls_999 DUM 0 1.008000 0.000A 0.00 0.00 So, I expect, this is, how it should look like. Be aware of the missing bonded terms in the force field for a DUM particle. Maybe, you want to call it H instead... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: Hi there, I met the problem when I ran "grompp", the errors are: ERROR 1 [file "po4lig4tip3.top", line 26741]: virtual site H21 (Res LG4-173) has non-zero mass 1.008 Check your topology. ERROR 2 [file "po4lig4tip3.top", line 26741]: virtual site H22 (Res LG4-173) has non-zero mass 1.008 Check your topology. Then I checked my topology file, here were the definition of LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms) ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 22 opls_9991 LG4 H22 22 0. 1.00800 opls_1720.4650 1.00800 in which opls_999 was from what I defined by myself in the force field itp file: opls_999 DUM 0 1.008000 0.000V 0.00 0.00 I changed the both of the mass_A to 0.0, but that didn't help. Does anyone have ideas on that? Thank you very much. Regards, Qin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] proper force fields for fullerene
Have a look at the manual and search the mailing list. You want to simulate a not recognized/parameterized molecule. Therefore you have to implement the parameters. How thats done can be found e.g. in the wiki. regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ serdar durdagi wrote: Dear all, I am trying to make MD simulation of fullerene derivatives with HIV protease..When I try to convert merged pdb file of protein+ligand to gmx file, using forcefields like G43a1 it gave error message as residue 'lig' not found in residue topology database. Is anybody knows which parameters in ff should I change? Kind Regards, Serdar Jetzt Mails schnell in einem Vorschaufenster überfliegen. Dies und viel mehr bietet das neue Yahoo! Mail <http://de.rd.yahoo.com/evt=40590/*http://de.docs.yahoo.com/ymail/landing.html>. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull code methods?
I'm no umbrella user, but as far as I know, you have to set different parameters, according to the manual. These may be similar to the AFM parameters, but still, in the config file, they are separated. Sure, you don't define a pull rate for Umbrella, because you build, as you said, discrete systems, where you put the umbrella potential onto one group along a reaction coordinate. It's clear that, depending on your system, you have to build N systems where your ligand is moved away from the protein along the reaction coordinate. Now, I'm curious about you asking about afm_init again...so you are finished with the umbrella business and want to do AFM now? The sentence, in fact, is very clear. You can break down the statement to: Calculate the resulting vector from the difference of two other vectors Therefore you have to find two vectors. One should be the COM of your reference group (you could also choose a single atom there...Just makes no sense to me) and one is either the COM of your ligand or, better, one single atom of your ligand, where the spring(AFM-tip) is attached to... I think, this has been discussed in the mailing list more than once... Maybe you should intensively search the archive for such things... regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi Maik, Thank you for the answer. I still have some questions. I still didn't get the umberalla sampling method. It seems to me AFM and umberalla are the same except that in umberalla we dont define a Pull rate. Looking at the literature, people have been using umberalla method with discrete simulations. i.e. 21 simulation windows. I kind of get the idea that you will have to manually set up the the 21 discrete simulations to get the final separated ligand-protein for the umberalla method? correct me if I am wrong. The other question I had is about init-afm position option. it says in the manual: afm init1 = Vector describing the initial position of the spring relative to the reference group. To start a simulation with zero initial force on the pulled group, the initial position should be set to the position of the pulled group relative to the reference group. This sentence is very unclear to me. how do u calculated the poition of the pulled group relative to the referene. Is is by calculating the Center of mass of the pulled group or by calculating the center of mass of the the whole system (pulled group + reference)? Thank you, Belquis Hi You have to tell GROMACS in the parameters-file (.ppa) which kind of PMF you want to calculate (runtype=afm,umbrella). Depending on this choice it's very likely that the afm_rate is simply ignored for umbrella, no? The force constant is mimicking the stiffness of the spring. You want to obey the stiff spring approximation (which still does NOT mean, you should use a rod ;) ) and therefore shouldn't choose the fc of the spring to small. I usually use a force constant of 500 kJ/mol*nm^2. It actually DOES make sense, to choose a fc comparable to the experiments, you want to compare your sim with, IF you want to compare :) Hope that helps Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Dear all, I have been reading the literature, mailing list and the manual. There is some questions that I cant understand: 1) there is three methods for the pull code: constraint force, AFM and umberalla. in both AFM and Constraint force, there is an option of the rate of pulling (contraint_rate, AFM_rate), however, for umberalla, there is only two options, a foce constant and position to be specified! my question is: how is the pulling controlled in umberalla sampling option? 2) if I want to do an AFM pulling...what is a reasonalble force constant to use? it seems people are using different K ranging from 10 to 1000's? thank u Belquis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx
Re: [gmx-users] Residue 'UNK' not found in residue topology database
Sorry, but first I suggest: Read the error message! Fatal error: > Residue 'UNK' not found in residue topology database Now, what could this mean? This actually means, in the forcefield residue database (e.g. ffoplsaa.rtp) exists no entry for a molecule named UNK... Rename the pdb to the expected name given in the rtp of the forcefield for your molecule, or if, more likely, the molecule really doesn't exist you have to build an entry by either building it from reasonable available building blocks or parameterize it yourself... And in general there's a very important rule to obey before posting to this mailinglist: RTFM... bye Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Sagittarius wrote: Dear Gromacs users, Could you please help me to find out what the problem is. I use command pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p outputName.top formaldehyde.pdb looks like this: COMPNDUNNAMED REMARK 1 PDB to MMOD atom-numbering translation table; the mmod numbers REMARK 1 pertain to the .dat file from which this file was created, REMARK 1 not to one created from this file: REMARK 1 PDB: 1 2 3 4 REMARK 1 MMOD: 1 2 3 4 / HETATM1 C01 UNK 0 0.000 0.302 0.000 0.00 0.00 0 HETATM2 O02 UNK 0 0.000 1.510 0.000 0.00 0.00 0 HETATM3 H03 UNK 0 -0.960 -0.262 0.000 0.00 0.00 0 HETATM4 H04 UNK 0 0.960 -0.262 0.000 0.00 0.00 0 CONECT134 CONECT12 CONECT12 CONECT21 CONECT21 CONECT31 CONECT41 END Gromacs output is --- Program pdb2gmx, VERSION Source code file: C:\Program Files\Microsoft Visual Studio\MyProjects\pdb2gmx\pdb2gmx\resall.cpp, line: 493 Fatal error: Residue 'UNK' not found in residue topology database --- Thanx for Using GROMACS - Have a Nice Day Thank you in advance Choose the right car based on your needs. Check out Yahoo! Autos new Car Finder tool. <http://us.rd.yahoo.com/evt=48518/*http://autos.yahoo.com/carfinder/;_ylc=X3oDMTE3NWsyMDd2BF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDY2FyLWZpbmRlcg-- > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull code methods?
Hi You have to tell GROMACS in the parameters-file (.ppa) which kind of PMF you want to calculate (runtype=afm,umbrella). Depending on this choice it's very likely that the afm_rate is simply ignored for umbrella, no? The force constant is mimicking the stiffness of the spring. You want to obey the stiff spring approximation (which still does NOT mean, you should use a rod ;) ) and therefore shouldn't choose the fc of the spring to small. I usually use a force constant of 500 kJ/mol*nm^2. It actually DOES make sense, to choose a fc comparable to the experiments, you want to compare your sim with, IF you want to compare :) Hope that helps Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Dear all, I have been reading the literature, mailing list and the manual. There is some questions that I cant understand: 1) there is three methods for the pull code: constraint force, AFM and umberalla. in both AFM and Constraint force, there is an option of the rate of pulling (contraint_rate, AFM_rate), however, for umberalla, there is only two options, a foce constant and position to be specified! my question is: how is the pulling controlled in umberalla sampling option? 2) if I want to do an AFM pulling...what is a reasonalble force constant to use? it seems people are using different K ranging from 10 to 1000's? thank u Belquis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: question about free energy. Gromacs user
Because you are quite greedy with parameters, one can just rougly assume that,e.g. your distance restraints are too short and therefore just kind of bend your ligand. Therefore it seems to find an energy minimum in modifiying some internal degrees of freedom to your restraint potential. Maybe you have to apply simply more distance restraints along the whole ligand. Maybe you should stick to methods like TI or pulling, which are implemented and heavily used within GROMACS... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Thank you David and Arneh for the comments. I just have a couple of things i want to clarify about the constrain distances i used. The distance I used to pull the ligand and receptor apart was a non-bonded distance between the amide nitrogen of the ligand and the oxygen carbonyl of the receptor (on both ends). looking at the slowgrowth results of my 5 ns, the distances i specifed increased from lambda 0 to 1, however, I didnt get separation as I wanted it since the ends just separated and the middle interaction of the ligand-receptor stayed intact. nothing unusal happened to the ligand or receptor. I dont think my method altered the internal degrees of freedom of the ligand. Can you please clarify this issue for me. I used constraint=all-bonds in my mdp file. Again, thanks you both for the comments. Belquis Maybe it should be obvious, but (a) why are you constraining two distances, and (b) are you sure your constraints aren't going to muck with the internal degrees of freedom for the ligand? I would think one would like to pull the ligand out of the receptor along some particular direction, but without doing anything to alter its internal degrees of freedom, or there would be a free energy associated with changing its internal degrees of freedom that you wouldn't capture in the PMF calculation. I agree with David's comments here. Check out the 'Special Topic' section of the GMX manual. you can either do a pulling simulation or umbrella sampling (where the position and constrain the ligand on some rxn coordinate, in several simulation). The output of such simulatsions is a *.pdo file, which you can then run g_wham on to obtain a PMF. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?
Be aware, that you can't use the ouput with every forcefield... Attaching the gro-file to your protein gro at the proper position (right after the protein) and building the correct topology should do the job. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ mjduan wrote: Yes, I found a server (ProDrg) can get the .gro and .top files of ATP molecule. --- Whereas one should also mention, that ATP isn't included in every forcefield, GROMACS supports... So probably, parameterization has to be done also. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Mark Abraham wrote: mjduan at smail.hust.edu.cn wrote: Dear GROMACS users: I want to simulate a complex composed by a protein and an ATP molecule, and when I use the pdb2gmx to build the topology file and transfer the*pdb* file to *gro* file, it said "/Fatal error: Atom PG in residue ATP 1 not found in rtp entry with 36 atoms while sorting atoms/", So how can I build the *top* file and *gro* file for ATP molecular and simulate the protein molcular and ATP molecule simultaneity? By reading chapter 5 of the manual thoroughly, understanding how the rtp files work for your force field and modifying your .pdb file and/or force field files to work suitably. Mark ___ gmx-users mailing listgmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?
As Mark suggested. If you have the parameters for your ATP, build an RTP-entry and afterwards, give the protein together with ATP into pdb2gmx... Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: > Thank u very much for your suggestion, and now I had get the .gro file > and .top file of ATP molecule, but how to I add the ATP molecule into > the .gro and .top files of the protein? (If I paste the ATP's datas to > the end of protein's file directly, and do genbox, then the result (.gro > /.top file) only contain the atoms of the protein and water.) > And is there any difference between the .mdp file to do grompp for this > complex and for the system only contain protein and water? > > > > > mjduan at smail.hust.edu.cn > <http://www.gromacs.org/mailman/listinfo/gmx-users> wrote: >>/ Dear GROMACS users: > />/ I want to simulate a complex composed by a protein and an ATP molecule, > />/ and when I use the pdb2gmx to build the topology file and transfer > />/ the*pdb* file to *gro* file, > it said "/Fatal error: Atom PG in residue > />/ ATP 1 not found in rtp entry with 36 atoms while sorting atoms/", So how > />/ can I build the *top* file and *gro* file for ATP molecular and simulate > />/ the protein molcular and ATP molecule simultaneity? > / > By reading chapter 5 of the manual thoroughly, understanding how the rtp > files work for your force field and modifying your .pdb file and/or > force field files to work suitably. > > Mark > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constrains and TI
That sounds more reasonable...:) In fact I like the idea of using distance restraints, but I still doubt, that will work... I would really suggest to use the TI method. If you apply it properly it should give reasonable results. With proper application, speaking about using soft-core for VdW (with good parameters), hardcore for qq, back and forth morphing for an idea of the hysteresis or using discrete TI instead of slow-growth, etc. you should get reasonable results. But depending on your perturbation size this could also be a hard task, to obtain correct numbers and not just building the famous costly random number generator... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Thank you for the reply, Sorry for the confusion of my two emails. I guess I was using the word "pulling" in the wrong context. Now after my extensive reading, what I meant is that i want to calculate the absoulte binding free energy of a ligand/receptor complex. I have read the manual over and looked at the tutorials, and came to the idea that i can constrain distances b/w the ligand and the receptor and input a distance for state B to vary the distance using lamda. (Manual 3.3 chapter 6 special topics, section 6.3 Calcuating the PMF using the free-energy code) I am using contraints type 2, which can be perturbed in free energy calculations. here is what I used in my calculation: [ constraints ] ; ai aj funct length_A length_B 44 258 2 0.2592.406 123 179 2 0.3292.334 I am currently running a 5ns using the slow-growth method to give me an idea of what happens to the system. I am also looking into using orientational-restrains and using a thermodynamic cycle instead of PMF of the unbinding of the ligand to receptor. please correct me if I am wrong. and thanks for ur help. Belquis Hi First, for the other topic you posted (which is probably somehow related to this one): Now, please be more specific with what you want to doYou wrote: "What I want to do is calculate the free energy difference of pulling the ligand away from the receptor" This is a pulling approach, where you would like to do AFM sims and afterwards use Jarzynski. If that is what you want, search the literature for Jarzynski and try to understand his theorem (you will see, one pulling sim is not enough for free energy calc). Then you wrote: "I want to do it using theromdynamic intergration using the Lamda 0/1 stuff" This is a totally different approach With both, you can ESTIMATE binding free energies. Still, both are very different in the way to setup a simulation in GROMACS. You WILL find out, how to do it by: 1. Reading the manual 2. Searching the mailing list 3. Using the GROMACS Wiki 4. Using some of the tutorials, which were posted, by e.g. David Mobley Now, coming to your idea about using distance restraints to "pull" the ligand away (its more of a push). I think (correct me if I'm wrong), that you can't use A and B state distance restraints in GROMACS (or better say, they will stay the same for both states). I'd suggest to use either TI OR AFM pulling. For sure, you could do both and see, if you get similar free energy differences with both methods... I don't think, you can calculate the free energy difference by using different distance restraints, anyway. Regards P.S. As I just saw it. Inform yourself about the difference between CONSTRAINTS and RESTRAINTS (there is an important one...) Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: hello all, is it possible to constrain a distance (or several) between a ligand-receptor complex inorder to simulate free energy change of separating the ligand from the receptor? I intend to use TI and lamda to do free energy calculations. any help is appreicated. Belquis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@g
Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?
Whereas one should also mention, that ATP isn't included in every forcefield, GROMACS supports... So probably, parameterization has to be done also. Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Mark Abraham wrote: > [EMAIL PROTECTED] wrote: >> Dear GROMACS users: >> I want to simulate a complex composed by a protein and an ATP molecule, >> and when I use the pdb2gmx to build the topology file and transfer >> the*pdb* file to *gro* file, it said "/Fatal error: Atom PG in residue >> ATP 1 not found in rtp entry with 36 atoms while sorting atoms/", So how >> can I build the *top* file and *gro* file for ATP molecular and simulate >> the protein molcular and ATP molecule simultaneity? > > By reading chapter 5 of the manual thoroughly, understanding how the rtp > files work for your force field and modifying your .pdb file and/or > force field files to work suitably. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > . > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dummy atom definition prob in FEP
Your system will explode. Actually I'm not sure, why that is, but probably, because some forces from the bonded terms are transferred to your mass-zero particle, which then accelerates infinitly fast...even though I would expect some division over zero error in the velocity calculation... Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: Thank you, Maik. I do want to do standard FEP and thank you for telling me that FEP don't go with virtual sites. It does help. BTW, may I ask you why I should define a none_zero mass for a dummy atom? Thanks, Qin On 8/8/07, *Maik Goette* <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote: Friend... What are you trying to do??? If you want to do standard FEP with growing something into dummy (NOT virtual site) or from dummy, you must not use virtual sites! Virtual sites in fact, have no mass; neither in A- nor in B-state. Please read the fManual about virtual particles, their usage and why they exist in GROMACS (hint, delocalized charge) As far as I know, you can't morph a virtual site to a real particle. I also think, It wouldn't make much sense, though. If you want to morph away e.g. a proton, define a dummy in the b-state, which has no LJ parameters (eps and sigma=0) and no charge, but still the original mass. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi- bpc.mpg.de <http://bpc.mpg.de> mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: > Hi, >Thanks for reply. It seems that specifying mass_B = mass_A doesn't > help to solve the problem. However, if I don't use the directory > [virtual_site#] the errors disappear! What's the result if I do this? > Is the directory necessary in the FEP calculation to define the dummy > atoms? > Thanks, > Qin > > On 7/20/07, *Stéphane Téletchéa* < [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> > <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote: > > Wang Qin a écrit : > > Hi there, > > I have a problems when I do a FEP calculation. > > Below is how I defined dummy atoms in the topology file: > > [atom] > > ;nr typeresnr residue atomcgnrcharge > > masstype_B charge_Bmass_B > > 21 opls_1721 LG6 H21 21 0.4650 > > 1.00800 opls_0 0. 0.00 > > 22 opls_1721 LG6 H22 22 0.4650 > > 1.00800 opls_0 0. 0.00 > > .. > > > > I think you need to specify the mass_B=mass_A, at least this is how it > is setup in the tutorials i've done (the one from Berk Hess and the > other one from David Mobley). > > I've also done calculations without setting the mass for B (like you > did) and did not encounter any problem, the error you're seing could > thus come from another part of your system. > > Cheers, > Stéphane > > -- > Stéphane Téletchéa, PhD. http://www.steletch.org > Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig > INRA, Domaine de Vilvert Tél : (33) 134 652 891 > 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 > ___ > gmx-users mailing listgmx-users@gromacs.org <mailto:gmx-users@gromacs.org> > mailto:gmx-users@gromacs.org>> > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > <http://www.gromacs.org/search> before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >
Re: [gmx-users] Constrains and TI
Hi First, for the other topic you posted (which is probably somehow related to this one): Now, please be more specific with what you want to doYou wrote: "What I want to do is calculate the free energy difference of pulling the ligand away from the receptor" This is a pulling approach, where you would like to do AFM sims and afterwards use Jarzynski. If that is what you want, search the literature for Jarzynski and try to understand his theorem (you will see, one pulling sim is not enough for free energy calc). Then you wrote: "I want to do it using theromdynamic intergration using the Lamda 0/1 stuff" This is a totally different approach With both, you can ESTIMATE binding free energies. Still, both are very different in the way to setup a simulation in GROMACS. You WILL find out, how to do it by: 1. Reading the manual 2. Searching the mailing list 3. Using the GROMACS Wiki 4. Using some of the tutorials, which were posted, by e.g. David Mobley Now, coming to your idea about using distance restraints to "pull" the ligand away (its more of a push). I think (correct me if I'm wrong), that you can't use A and B state distance restraints in GROMACS (or better say, they will stay the same for both states). I'd suggest to use either TI OR AFM pulling. For sure, you could do both and see, if you get similar free energy differences with both methods... I don't think, you can calculate the free energy difference by using different distance restraints, anyway. Regards P.S. As I just saw it. Inform yourself about the difference between CONSTRAINTS and RESTRAINTS (there is an important one...) Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: hello all, is it possible to constrain a distance (or several) between a ligand-receptor complex inorder to simulate free energy change of separating the ligand from the receptor? I intend to use TI and lamda to do free energy calculations. any help is appreicated. Belquis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Mutagenesis
Hi The question arises, is "physically acceptance" equal to "biological reality" and the answer is (with reasonable probability) no. What I suppose, you want to do is calculating the affinity difference (free energy difference) for binding of a slab of DNA to a protein with "mutated" aminoacids. Therefore you will calculate via TI or so the difference in free energy of two states, where A is the one with the original AA and B with the "mutated" AA. With GROMACS, you can morph between these states and calculate the DeltaG. To get the atoms of the B-state positioned correctly, you may setup a library of your AAs and fit the backbone atoms to the BB-atoms of the original one. Then you have more or less reasonable positions for you B-state side-chain atoms. Afterwards have a look which side chain atoms of the B-state AA you really have to grow and afterwards start the sim. Which kind of TI one should use is hard to say, but I'd suggest discrete TI (not slow growth), because your B-state has the time to equilibrate (more or less) properly. If all this is feasible, one probably can't answer. At last, that's the best one can doand, btw., expect to invest some time to get this working. Hope, this helps. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Esther Caballero-Manrique wrote: Hi everyone, I am new to mutagenesis studies, so I was wondering if I could get some input on my approach. My task involves mutagenizing a residue (with all 19 possibilities) in a protein that binds DNA, and then deciding whether the resulting structure is physically acceptable. My approach to do this is 1) mutate using MODELLER, 2) check the structure with something like PROCKECK (although since I am just mutating one residue, this doesn't seem important/useful), 3) align the resulting structure from MODELLER with the original and paste the DNA 4) check for clashes with PROCHECK, and 5) do MD to see whether the model is feasible/calculate free energy of binding. Obviously all steps are easy and fast except the last one, and my question is, does anyone think that step 5 is overdoing it if one just needs to know whether a structure is feasible ( i.e., I am not using MD for refinement, but as a check of the feasibility of the complex)? Does anyone have a better/easier way to do this? Thanks a lot for your help, Esther -- Esther Caballero-Manrique Unit of Cancer Pathology Center for Excellence in Research on Aging University "G. D' Annunzio" Via Colle dell' Ara 66013 Chieti Scalo (Chieti), Italy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dummy atom definition prob in FEP
Friend... What are you trying to do??? If you want to do standard FEP with growing something into dummy (NOT virtual site) or from dummy, you must not use virtual sites! Virtual sites in fact, have no mass; neither in A- nor in B-state. Please read the fManual about virtual particles, their usage and why they exist in GROMACS (hint, delocalized charge) As far as I know, you can't morph a virtual site to a real particle. I also think, It wouldn't make much sense, though. If you want to morph away e.g. a proton, define a dummy in the b-state, which has no LJ parameters (eps and sigma=0) and no charge, but still the original mass. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: Hi, Thanks for reply. It seems that specifying mass_B = mass_A doesn't help to solve the problem. However, if I don't use the directory [virtual_site#] the errors disappear! What's the result if I do this? Is the directory necessary in the FEP calculation to define the dummy atoms? Thanks, Qin On 7/20/07, *Stéphane Téletchéa* <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote: Wang Qin a écrit : > Hi there, > I have a problems when I do a FEP calculation. > Below is how I defined dummy atoms in the topology file: > [atom] > ;nr typeresnr residue atomcgnrcharge > masstype_B charge_Bmass_B > 21 opls_1721 LG6 H21 21 0.4650 > 1.00800 opls_0 0. 0.00 > 22 opls_1721 LG6 H22 22 0.4650 > 1.00800 opls_0 0. 0.00 > .. > I think you need to specify the mass_B=mass_A, at least this is how it is setup in the tutorials i've done (the one from Berk Hess and the other one from David Mobley). I've also done calculations without setting the mass for B (like you did) and did not encounter any problem, the error you're seing could thus come from another part of your system. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org <mailto:gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search <http://www.gromacs.org/search> before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] free energy perturbations and B-parameter specifications
Hi
You have to be more specific...
Did you just do one sim for Gly->Ala?
Are you sure, you did the simulations in a way, you can compare it to
exp. results? (think about doing the perturbation once in water and once
in vacuum or so)
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Soren Enemark wrote:
Dear Gromacsers,
I have been doing free energy perturbations Gly->Ala in one strand of
collagene.
Now, the problem is that I have later closely reread the section 5.6.4
("Free
Energy Calculations") p. 105 in which it says:
"Bonded interactions between atoms that are not perturbed do not need B
parameter specifications ..".
My questions are:
1. Does this mean that bonded interactions between atoms that ARE
perturbed DO need B parameter specifications? Even if they are the same
in state
A and B?
2. What about the other topology parameters (angles, dihedrals etc), do
they need to be specified too?
3. What happens if I have not specified these specifications?
The relevant parts of the topology file which I use are:
[ atoms ]
87 N 13ALA N 49 -0.2814.0067 ;
qtot 0.72
88 H 13ALA H 49 0.28 1.008 ;
qtot 1
89CH2 13ALA CA 50 0 14.027
CH1 0.0 3.019 ; qtot 1
90DUM 13ALA CB 50 0 15.035
CH3 0.0 15.035 ; qtot 1
91 C 13ALA C 51 0.38 12.011 ;
qtot 1.38
92 O 13ALA O 51 -0.3815.9994 ;
qtot 1
...
[ bonds ]
...
8789 2gb_20
8990 2gb_26
8991 2gb_26
...
[ angles ]
858789 2ga_30
888789 2ga_17
878990 2ga_12
878991 2ga_12
908991 2ga_12
899192 2ga_29
899193 2ga_18
And so on, ie, no B specifications have been done except for the atoms!
Best regards, and thank you in anticipation,
Soren
Ps. One (non-gromacs -sorry) question, given that the above is not wrong:
For the pertubation Gly->Ala I have get a deltaG of 0.8 kcal/mol.
Looking through literature, this does not seem all wrong, say if the
pertubation took place in an alpha-helix. On the other hand, it is
close to the thermal energy (~kT), and a previous article doing the
exact same perturbation arrives at a deltaG around 8.6 kcal/mol. Could
anyone comment on that?
Alt i én. Få Yahoo! Mail <http://dk.mail.yahoo.com> med adressekartotek,
kalender og notesblok.
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Re: [gmx-users] free energy calculation and constraint distance?
Sorry, I really didn't get, what your goal is and what, in fact, you really want to do. For free energy calculations, you can - either do Thermodynamic integration (the lambda 0/1 stuff) - or pulling (force probe) and afterwards use Jarzynskis theorem - or umbrella sampling together with WHAM (if I remember correctly) Now, it's up to you, which method you favormay also depend on your system/question Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hello Gromacs users, I am trying to do a free energy calculation, which I have never done before. I have read the manual and the tutorial on the wiki but there is still some issues not clear to me. I am trying to calculate free energy difference of pulling the ligand from a beta-sheet receptor. I understand there is a pull code with different options or it can be done with constraint distances. Please correct me if my procedure is wrong: I want to constraint several distances between the ligand and the receptor and then increase that distance to one where the ligand and receptor are completely separated. For that, I would have to modify my topology where i define [ constraints ] for the distances i want to constrain between the ligand and the receptor and input the bond length for state A(lamda=0) and state B (lamda=1) for each. will the distances defined move the whole ligand away from the receptor? since am only defining several distances between ligand and receptor only. or is it recommended to use the pull code? Any directions is appreciated. Belquis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about DNA simulation
Hi I never had to change masses in the nb.itp and I ran lots of simulations with the amber-Port...Are you sure, that you had no dummies with mass zero or so? REgards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ George Abadir wrote: Hi, Actually I think that although the .atp file seems to be used, the masses in the ffamberxxnb.itp file must be changed from the zero values to the correct ones: when I ran a simulation without changing them I got infinite velocities and which did nor happen when I changed the masses to the correct ones. Thanks, George David van der Spoel wrote: Maik Goette wrote: David I think, I should not contradict to one of the developers, but if your statement is true: 1. Where, in fact, are the masses coming from (the masses in the amberFF port can only be found in the atp, as far as I know)? 2. Why does GROMACS complain about missing atoms in the atp-file, if I add a new atom type to the nb-section? Just out of curiosity... Hm, no problems contradicting me at least... I presume you're right. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about DNA simulation
David I think, I should not contradict to one of the developers, but if your statement is true: 1. Where, in fact, are the masses coming from (the masses in the amberFF port can only be found in the atp, as far as I know)? 2. Why does GROMACS complain about missing atoms in the atp-file, if I add a new atom type to the nb-section? Just out of curiosity... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ David van der Spoel wrote: Maik Goette wrote: Because it is? The masses are defined in the .atp file. I dont't know how GROMACS handles the stuff, but that is sufficiantMaybe Eric was a bit lazy... Why do you care for that...? atp file is never used... Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ bo yang wrote: Hello, I have a question regarding DNA simulation. I have the amber99 package. Can anyone give me an explanation why all the masses in the ffamberXXnb.itp are 0? Thank you very much! Bo ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about DNA simulation
Because it is? The masses are defined in the .atp file. I dont't know how GROMACS handles the stuff, but that is sufficiantMaybe Eric was a bit lazy... Why do you care for that...? Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ bo yang wrote: Hello, I have a question regarding DNA simulation. I have the amber99 package. Can anyone give me an explanation why all the masses in the ffamberXXnb.itp are 0? Thank you very much! Bo ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Total energy with different energy groups
Random velocities? Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Daniel Cheong wrote: Thanks for your reply. I thought so too, but i have checked it several times. The only thing i changed was the "energygrps =" line in my .mdp file. Then the inclusion and exclusion of energy monitor groups or just specifying different energy groups will result in a different total energy. And the larger the energy group, the greater the difference when compared to the energy calculated with no energy monitor groups. i use the exact same initial configuration, topology, index files. Mark Abraham wrote: Daniel Cheong wrote: Hi, I am trying to calculate the initial energy of some molecular configuration that I have. I have also defined some energy groups. This gives me a set of energy values. However when I changed the energy monitor groups, and repeat the calculation on the same configuration, i get a different total energy. This seems strange to me. I was under the impression that while the mutual interactions of the energy groups will of course be different, the total energy of the system should be the same regardless of what energy groups I define. Is that right, or am i missing something altogether? Thanks for any help. Probably you're not doing the same calculation. You are right, in that the energy monitor groups will not affect the calculation of the total energy. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with forcefield amber99 in Gromacs
Have a look into the tar again... Maybe ffamber_tip3p.gro is what you are searching for And to specify Mark's comment: You may want to include ffamber_tip3p.itp in your topology file. A further suggestion: Don't think, a software can undertake the thinking for you...We all are waiting for the Do-whatever-I-mean-tool... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ bo yang wrote: Hi, I have a question regarding to using forcefield amber99 in Gromacs. I have all the parameter files of amber99. I am doing the MD of carbon nanotube with DNA. I have changed the .pdb file of the DNA according to the instruction. I generated the topology of DNA with identifying -water tip5p.gro. The topology file of DNA is also generated successful. Pymol is used to visualize the DNA structure. Now, I am doing the energy minimization. When I use the grompp command, the output is that "Fatal error: No such moleculetype SOL". I am wondering can anybody tell me how to use the tip5p model of water. Also, actually, I want to do the simulation with tip3p. But I could not find tip3p.gro. I checked back. There was also another person asked the same question. But, I don't quite following the answer. Do you minding telling me more about the process? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] FEP with real or dummy charges?
No. I said, you may want to perturb all partial charges in the site, where the netto +1 charge sits OR place a virtual site somewhere in between, to grow a point charge, whereas I'm not sure, if a point charge is, what you want. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Georgios Patargias wrote: Many thanks for your reply! Concerning the use of PME, I also put a counter charge in bulk in order to keep the whole cell neutral. So, if I understood corectly, you suggest that I should perturb all the partial charges around the vitual site? George -Original Message- From: [EMAIL PROTECTED] on behalf of Maik Goette Sent: Sat 5/19/2007 12:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] FEP with real or dummy charges? I don't really know, if this may solve your problem, but what I want to suggest is, not using PME for the simulation. I don't know, how other longerange-methods behave while changing the total charge of the system, PME won't work (as far, as I know). Concerning your way, how to perturb the charge, it depends on, where you think the charge sits...In general, I would assume, that a site, where a netto charge is 0 and the same, where the netto charge is one, will be different in partial charges of most atoms in the area. Therefore perturbing the whole site (just the partial charges) would be the right way to do it. This in fact means, that you have the partial charges for the +1-charge atoms...maybe spreading the charge in a senseful way, should do it. Using a virtual site would be the solution for a point charge in space, its coordinates relative to two or more atoms. If you want to have the charge sitting on a special atom, just change that charge explicitly, although I'm really not sure, if that's the way, one should go. Hope you get some help from that. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Georgios Patargias wrote: Hi I want to calculate the change in free energy (electrostatic contribution only) when introducing a charge in a certain site of a protein using a single step FEP. Should this be done with charging an inserted virtual site (a dummy atom) or a protein atom (e.g. Ca)? I noticed that in the case of the dummy atom, the Coul-14:Protein-vsite zero. I am not sure why though... Thanks a lot in advance for any feedback. Best wishes George Dr. George Patargias Polymer IRC Group University of Leeds Leeds, LS2 9JT, UK ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] atom type not found error
Hard to tell from that amount of information... Seems, you don't include a forcefield... Please describe in more detail, what you exactly did and maybe post the head of your topology-file... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ mahbubeh zarrabi wrote: Hello everybody; when I try to create the .tpr file from my .gro and .top files, using command "grompp", there is an error saying atomtype (e.g. OS) not found. when I look at the .atp file at gromacs directory,the atom types and their corresponding masses exist there.what could be the problem and how can I solve it? thank you in advance Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge to see what's on, when. http://tv.yahoo.com/collections/222 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] antechamber installation
Just wanted to mention that ;) Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Tsjerk Wassenaar wrote: Hi Francesco, On 5/19/07, Francesco Pietra <[EMAIL PROTECTED]> wrote: Is it a script equivalent to .cshrc (as in antechamber web page) available for bash? I am unfamiliar with csh. .bashrc While the 64bit machine (Linux Debian amd64 etch dual-core opterons) were to run gromacs is busy, I want to try to install antechamber on a 32bit machine (Linux debian i386 etch Athlon single processor) well equipped for graphics, OpenGL etc. At any event, I would prefer to have antechamber on the 32bit because I refrain installing the X system on the 64bit machine. The two machines "talk" with one another through ssh, and it is possible to install the ROOT package for monitoring. I'm not completely sure whether you mean to have another question in here :S In any case.., note this is a gromacs user list, and with questions regarding antechamber and linux you're a bit out of scope here... Cheers, Tsjerk ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] FEP with real or dummy charges?
I don't really know, if this may solve your problem, but what I want to suggest is, not using PME for the simulation. I don't know, how other longerange-methods behave while changing the total charge of the system, PME won't work (as far, as I know). Concerning your way, how to perturb the charge, it depends on, where you think the charge sits...In general, I would assume, that a site, where a netto charge is 0 and the same, where the netto charge is one, will be different in partial charges of most atoms in the area. Therefore perturbing the whole site (just the partial charges) would be the right way to do it. This in fact means, that you have the partial charges for the +1-charge atoms...maybe spreading the charge in a senseful way, should do it. Using a virtual site would be the solution for a point charge in space, its coordinates relative to two or more atoms. If you want to have the charge sitting on a special atom, just change that charge explicitly, although I'm really not sure, if that's the way, one should go. Hope you get some help from that. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Georgios Patargias wrote: Hi I want to calculate the change in free energy (electrostatic contribution only) when introducing a charge in a certain site of a protein using a single step FEP. Should this be done with charging an inserted virtual site (a dummy atom) or a protein atom (e.g. Ca)? I noticed that in the case of the dummy atom, the Coul-14:Protein-vsite zero. I am not sure why though... Thanks a lot in advance for any feedback. Best wishes George Dr. George Patargias Polymer IRC Group University of Leeds Leeds, LS2 9JT, UK ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Residue 'SIA' not found in residue topology database
Right, Mark But do you think, deleting something is the way, how to do it? ;) Maybe it could be problematic, if this molecule is, what they want to simulate in the protein... Kong, a first step (maybe nothing for Newbies, thats for sure) would be to make some QM-calculations with e.g. Gaussian or try Antechamber (?) from the AMBER-package. After calculating reasonable partial charges, you can try to get the LJ-Parameters and other stuff from existing FF-entries. How to build the FF-entries, i.e. mainly an RTP-entry, one can obtain from the manual. Happy LEGOing Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Mark Abraham wrote: > kong.winter wrote: >> Hi all, >> when I use the following command:"pdb2gmx -f 1G1T.pdb -p gr.top -o gr.gro" >> There's a fatal error: >> Residue 'SIA' not found in residue topology database >> >> I checked the PDB file, the following details: >> HET SIA C 601 20 >> HETNAM SIA O-SIALIC ACID >> FORMUL 2 SIAC11 H19 N1 O9 >> .. >> >> >> Who knows how to solve it? >> Any tip is appreciated, thank you very much. > > This means what it says: the force field you're using doesn't have an > entry for residue SIA, which is apparently sialic acid. If you want to > simulate with this molecule in the system, you'll need to develop a > topology for it (and maybe parameters - this is not encouraged for > newcomers), and put that into the .rtp file (read chapter five). > Otherwise, delete it from your .pdb file. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > . > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems using grompp and amber force field
Yes, the 3.3.1 amber-FFs should be used, because the implementation of the QM/MM parts changed the format in some FF-parameters files. I would suggest, not to use the OPLS-DNA parameter set, because it isn't published, yet (as I know) and also uses RESP-charges, which may also be problematic with OPLS. Using the amber-port is, in my opinion, the best way to handle DNA/RNA (in GROMACS). I fear, I can't really help you with your error, but did you try the amber99 FF? I use that and never ran into such errors. Did you had a look, if your total charge is more or less an integer? If not, one proton in your first base may be the wrong type...but this shouldn't result into your error. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ root wrote: Dear GROMACS user: Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of http://folding.stanford.edu and now I understand your comments. We tried with cpp = /lib/cpp -traditional in the mdp file. The warning desapears, but the error messages is similar. (Fatal error: Atoms in the .top are not numbered consecutively from 1 --- We tested the dick.top file, and we verified that the atoms are numbered consecutively from 1 to 758.) We download the ffamber_v3.3.1-doc.tar.gz, that we considered that correspond to the 3.3.1 version of GROMACS. Is this correct? Thanks in advance. Mario El lun, 07-05-2007 a las 23:17 +0200, Erik Marklund escribió: As someone already mentioned, the following can be found among the AMBERport FAQ: >> Why do I get a grompp warning "missing white space after `#define proper_*'?" Set "cpp = /lib/cpp -traditional" in your .mdp file to remove these warnings, which result from the use of the N* atom type of the AMBER family of force fields and can be ignored. << Did you try doing that? Good luck! /Erik 7 maj 2007 kl. 22.29 skrev root: Hi, I think if you set "cpp = /lib/cpp -traditional" in your .mdp file then it should get rid of the warnings about "spaces are absent in target after the name of macro". For more info see <http://folding.stanford.edu/ffamber/FAQ.html> Tom --On 07 May 2007 20:42 +0200 David van der Spoel <[EMAIL PROTECTED]> wrote: David and GROMACS users: Sorry we changed the error message in ... /usr/local/gromacs/share/top/ffamber03bon.itp:541:22: warning: spaces are absent in target after the name of macro because of the original message was in spanish. We checked these files above. We run GROMACS in fedora 6.0 We analyzed the warning messages. They correspond to a format of description of a dihedral angle. For example the 538:22 warning correspond to le line 538 column 22 #define proper_X_CT_N*_X and there are a format problem with the * symbol. we don't know that to do still with this. Thanks in advance root wrote: De: David van der Spoel <[EMAIL PROTECTED]> Responder a: Discussion list for GROMACS users Para: Discussion list for GROMACS users Asunto: Re: [gmx-users] Problems using grompp and amber force field Fecha: Mon, 07 May 2007 20:42:51 +0200 (15:42 ART) The procedure to simulate the DNA dodecamer was: 1) We generate the DNA topology and coordinates in gromacs format (with the amber03 force field ) using the pdb2gmx program: pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce 2) and we obtain the box with the dodecamer plus water coordinates using editconf and genbox: editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle 90 90 90 genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top 3) with the files dick03.pdb and dick.top we run grompp: grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top The output of the program indicate ... creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20# checking input for internal consistency... calling /usr/bin/cpp... In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19, de dick.top:11: /usr/local/gromacs/share/top/ffamber03bon.itp:538:22: warning: spaces are absent in target after the name of macro /usr/local/gromacs/share/top/ffamber03bon.itp:541:22: warning: spaces are absent in target after the name of macro /usr/local/gromacs/share/top/ffamber03bon.itp:543:22: warning: spaces are absent in target after the name of macro /usr/local/gromacs/share/top/ffamber03bon.itp:547:21: warning: spaces are absent in targe
Re: [gmx-users] soft-core potential in combination with PME (sorry, again)
David Mobley wrote: > If I remember correctly, basically what the Anwar paper tries to > achieve is separately smoothing the two. You could probably accomplish > the same thing by allowing separate sc-alpha and sc-power for Coulomb > and LJ interactions so they can be tuned separately. I would suggest to implement exactly that in the version 4. As David mentioned, there CAN occur problems with the differing parameters. In contrast to David, I experienced no general benefit in using different parameters for coulomb and vdw, what may be somehow my fault, or, more likely (maybe also less ;) ), depend on the system one perturbs. If you would change the code somehow, that the parameters can be modified independendly, I would also suggest to implement a sort of sigmoidal behaviour for the lambda change. We did that for the 3.3.1 code, so I could, at least, provide you with the basic code for that. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Which force-field for DNA-protein complex ?
I'm using amber99 port most of the time. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ mathieu coincon wrote: I searched the database in order to choose which ff I should use. But I would like to have feadback from people used to such simulations. Thanks by advance --- Mathieu Coincon PhD Student Universite de Montreal (+1)514-343-6111 #5352 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Thiophosphate LJ-Parameters
I'm searching for LJ-parameters for a sulphur bound to phophorous in a thiophosphate. I tried some literature search, but didn't find anything, except some statement of 1985, that in this case the negative charge is shifted to the sulphur (our QM calculations don't agree with that, anyway). Now, the question arises, which LJ-parameters for sulphur to choose. In OPLSAA, there are some anionic sulphur LJ-parameters (which are not in the amberFF, but I guess, they could simply be ported)...still, I don't feel well, using those, because, our QMs clearly show, it's no sulphur anion. Does anyone have any hints towards thiophosphate paramters (literature, chemists intuition ;) ), or at least an idea, which amberFF-sulphur I can use, without getting in to much trouble? Furthermore, exactly this sulphur should undergo TI, which even makes things worse, concerning correct parameters. Best regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] oplsaa with tip4p
Probably you have to rename MW to HW3 in your pdb-file...it's a known issue, I guess. Best regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Christian Seifert wrote: Hi. I want to use the ff oplsaa with tip4p water (as suggested in the manual). Using: genbox_d -cp hpo4_box.pdb -o hpo4_water.pdb -cs tip4p.gro creates a good pdf-file with tip4p-water, but the following: pdb2gmx_d -f hpo4_water.pdb -o hpo4_water.gro -p hpo4_water.top -ff oplsaa -n hpo4_water.ndx -water tip4p brings up this error: --- Program pdb2gmx_d, VERSION 3.3.1 Source code file: pdb2gmx.c, line: 393 Fatal error: Atom MW in residue HO4 1 not found in rtp entry with 4 atoms while sorting atoms --- Is there any workaround? Thanks in advance Christian Seifert. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Nucleic Acids -- Protonate ?
> I don't know how to solve your problem, but merely adding counter-ions > because you don't know where or how many hydrogens there might be is > almost guaranteed to lead to a simulation that has no correlation with > reality. The answer to the problem has been presented (amber FF port), but I thought exactly the same...and btw...Mark, the one with the car mechanic was great...;) Best regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Mark Abraham wrote: Viswanadham Sridhara wrote: Hello, I wanted to perform MD simulation on a DNA structure I found from RCSB.org. After changing C, G, A, T to DCYT, DGUA, DADE and DTHY respectively, I used pdb2gmx to create topology file. It says missing hydrogens, which is obvious and I realized I could not use protonate command as ffgmx2.hdb does not have these residues to be protonated. Is there any other file to add missing hydrogens or Is there any other program which you can use to add missing hydrogens to nucleic acids. The total charge now is -43e, which is quite huge, and I am looking to see electric field effects on the DNA. This will be a lot of charge to neutralize by adding counter-ions, if I ignore hydrogens. I don't know how to solve your problem, but merely adding counter-ions because you don't know where or how many hydrogens there might be is almost guaranteed to lead to a simulation that has no correlation with reality. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] free energy calculation
You are probably starting your runs from a non equilibrated structure. Assume, the system changes via a slow growth run. The atoms may rearrange due to changes in their potentials. Therefore it may be problematic, if you start from the same structure for different lambdas. Try simulating a one way slow growth and pick the snapshots close to your lambda value from the trajectory and start your "quasi-FEP" with those. I can't answer your second question properly, because I don't know the code itself. But my guess is, that GROMACS calculates the potential for state A and B and then interpolates between them in a linear fashion (dependent of if you use soft-core or not). From this arises a yes for the second part of your question. If I'm wrong with that, I'm sure, someone who knows better will correct me quite fast. ;) Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Paolo Cerri wrote: Dear all, I'm trying to calculate free energy differences using the standard method of thermodynamic integration.I calculate dG/dlambda for different values of lambda and then integrate. When decoupling LJ interactions i have LINCS WARNING: Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.007366 (between atoms 7 and 8) rms 0.002535 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7 8 50.10.1010 0.1017 0.1010 9 10 65.80.1090 0.1085 0.1090 17 18 32.10.1010 0.1011 0.1010 17 19 32.00.1010 0.1011 0.1010 [...] and eventually the simulation stops (during the equlibration run at lambda >= 0.9) I obtain the following message: - Program mdrun, VERSION 3.3.1 Source code file: clincs.c, line: 559 Fatal error: Too many LINCS warnings (10001) - aborting to avoid logfile runaway. This normally happens when your system is not sufficiently equilibrated,or if you are changing lambda too fast in free energy simulations.If you know what you are doing you can adjust the lincs warning threshold in your mdp file, but normally it is better to fix the problem. -- I remark that in my simulations lambda is not changed continuously during simulation, but i perform several simulations at different fixed lambda values. I change only LJ interactions (having previusly turned of Coulomb interactions) I use Amber forcefield ffamber99 thanks in advance Paolo ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS AMBER DNA TERMINUS
I guess you misunderstood that. What you have there, is the terminal hydrogen, which is an hydroxyl one and therefore fully ok. You should search for an atom at the nucleobase, which has atom type 25. This usually has to be changed. Strange error, though :) I think its somewhere around N1 for guanines, e.g. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Andreas Kukol wrote: Dear All, I am using Gromacs 3.1.1 with the AMBER port. After following the instructions on the ffamber web-page, pdb2gmx works fine. But according to point 6: "... However, for nucleic acids this also often causes pdb2gmx to replace an H atom in the first residue of all nucleic acid chains with an incorrect H atom, resulting in non-neutral charge. The correct atom is generally replaced with an atom of type amberXX_25 (hydroxyl H), as pdb2gmx treats it as a terminal hydrogen ..." Indeed I find this atom in the first residue: 1 amber99_25 1DG5H5T 1 0.4422 1.008 ; qtot 0.4422 The solution given (a) is to correct the atom type and charge in the .top file by hand. My question is: What is the correct atom type and charge for this hydrogen ? The ffamber03.rtp contains exactly this atom type and charge in the specification for the residue DG5. So it should be correct ?? Many thanks Andreas ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about afm !
Sending a message again, won't help you, if you don't follow the Marks' suggestions. And please, not again a discussion about politeness...;) This is, what he wrote: hi everyone > I need to pull the two parallel monolayers together,the two monolayers > are in the x-y plane , so i pull the one along the z direction,but it > stay still! i tried several times ,but all failed! > i use the > [position_restraints ] > 1 1 9 9 4000 > 2 1 9 9 4000 > the 1 and £²¡¡are the atoms in the long molecules that form the monolayers > ,if i decreased the fx,fy,fz,it show core fault and stopped! > the ; Force constants in kJ/(mol*nm2) > afm_k1 = 10 > who can tell me why! I can't even understand your statement of your problem, never mind understanding the problem or helping to solve it. If you want people to give free help, please write clearly, in full sentences, describing what you wanted to do, what you actually did, what the error messages actually were, and do all of the above using sensible characters in sensible fonts. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: hi all in my model ,in order to simulate a LB monolayer adsorb on base ,the monolayer composed of 108 c17cooh that in a plane ! i need to pull the monolayer!how can i to pull the monolayer along the z direction while keep the molecular in a plane ！ 想免费获得高速稳定的3G邮箱吗？ www.126.com <http://www.126.com/> ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] AMBER atom type for Hydroxamate moeity
Maybe, one could also think about calculating the RESP charges via QM, e.g. with Gaussian...Further parameters, like force-constants and dihedrals could also be evaluated... But what's against an expensive random number generator? I fear I'm doing this with FEP all day long...;) Raja: We are (mostly) not doing LEGO here. You should inform yourself about the theoretic parts in general. Then you would see, that LEGOing a molecule can't be feasibleI suggest e.g. Leach, Molecular Modelling, Section 3: Empirical force field models. There you can find lots of information about what MD in general resembles. Best regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Mark Abraham wrote: raja wrote: Dear gmxions, I am writing a topology for a ligand using AMBER99 force field convention. The ligand contains the hydroxamate group, for your quick reference I have drawn it below O HO|| \ / \ N Your N has an unsatisfied valence... what's missing? (Don't bother to tell me, it doesn't matter) Please let me know which atoms type in amber can be used for these atoms Especially the Nitrogen atom in this group. Since I am using carbonyl group and hydroxyl group atoms types for oxygen (But I am not sure of its validity). Please help me to chose appropriate atoms type. Probably, none of them. Force fields are not magic numbers that can be applied to all possible "types" of atoms. They are constructs designed to be reliably applicable to fairly narrow sets of atom types under the range of conditions they were parametrized with (also normally narrow). You will see this when you read the paper that describes the development process of this force field. Notwithstanding, people routinely abuse them with gay abandon, probably on the bad advice of others, or their own experience of the fairly good transferability of quantum-chemical methods. Your only vaguely reliable course is to find a set of experimental data consistent with those used for the development of the force field, work out what new values you need to derive and to follow a process to optimize those values to reproduce the experimental data. This process is not for the inexperienced, or for the faint of heart. Otherwise, you'll have the usual expensive random number generator. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Partial charge distribution for metal ligating atoms
Hi Depends on your system, but in principle yes. A Cystein should be neutral. If you take a deprotonated one to build a complex with the zinc, it should be neutral afterwards. Lets assume a case with HIS/HIS/CYS as complex partners. the resdiues without a complex are assumed to be neutral. Therefore, their charges added should be 0. Add your zinc to the complex, take a partial charge of 0.7xx for it and modify the charges of the complex partners (i.e. the S and in the case of histidine it makes sense to spread the charge difference over the ring). If you now add up all the charges of all complex partners, the system should again be at charge 0. I can't see the problems, sorry. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ raja wrote: Dear Mark, Thanks for your reply. Well, I have well taken your point of making separate charge group constituting Zn and its residues and I am working out for it, in mean time I need some clarification in my present approach. I just detailed out my earlier mail hereunder. I am using AMBER force field. This is default partial charge distribution for deprotonated Cystine CYM N -0.4157 CYM H 0.2719 CYM CA -0.0351 CYM HA 0.0508 CYM CB -0.2413 CYMHB1 0.1122 CYMHB2 0.1122 CYM SG -0.8844 CYM C 0.5973 CYM O -0.5679 Formal Charge = -1.0 Now my modified partial charge at SG to -0.6944 CYM N -0.4157 CYM H 0.2719 CYM CA -0.0351 CYM HA 0.0508 CYM CB -0.2413 CYMHB1 0.1122 CYMHB2 0.1122 CYM SG -0.6944 CYM C 0.5973 CYM O -0.5679 Formal Charge = -0.8100 --- According to manual, to ensure integer value of total charge on the residue CYM (cysteine). Ideally, following the force field convention, I would like to do readjustment of the individual partial charges to make it as total = -1. But on other hand this is my intuition that, formal charge for -1 for CYM is applicable for free Cysteine residue in AMBER force field, but in my case, it is harmonically bonded with zinc and also the charge transfer is taken place. This makes me to think that the formal charge of CYM should be adjusted to neutral. Please give your thought? With thanks ! B.Nataraj On Tue, 28 Nov 2006 17:51:04 +1100, "Mark Abraham" <[EMAIL PROTECTED]> said: raja wrote: Hi gmxions, There are many references, say that Zn2+ partial charge should be reduced to ~0.7 rather than the force field default value of 2. In line with that there are many values published for distributed charge in its surrounding ligand atoms in compensation for loss of positive charge of Zn. OK, so this strategy preserves charge neutrality over the zinc and a bunch of ligand residues. It will not preserve charge neutrality of the individual residues, obviously. Now I am having set of values to be distributed for my system's active site residues, say for one SG-Cys, and two NE2-His atoms. My question is that what will be net formal charge for these residues after its specific atoms' charges are modified. The old value, plus the modification? In other words, for example, after modifying default partial charge of SG-Cys from -0.8844 to -0.6944, Should I adjust its net formal charge to -1 or to 0? Not sure where you're adjusting the "net formal charge" or why you think it's necessary. What you really want to do is have charge groups with integral values of charge (see section 3.4.2 and some part of Chapter 5 for how to do this), so that probably means combining the zinc with chunks of these residues into one large +2 charge group. Then on what basis I can adjust rest of the atoms’ partial charges. Why would you do this? Whatever you do should be consistent with the most reliable scheme in the literature, unless you want to create an expensive random number generator. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users P
Re: [gmx-users] protonated cys -S
Try renaming the Cys in the the PDB to CYS2. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Giacomo Bastianelli wrote: Hi Tsjerk, the distance of the "not formed" S-S is 0.202 while the two "formed" S-S are 0.204 and 0.203. Therefore, gromacs should recognize all three and create the SS bonds. CYSSG1CYSSG10.2CYS2CYS2 this is the second line of my specbond.dat Thanks, Giacomo Tsjerk Wassenaar wrote: Hi Giacomo, The two sulphur atoms have to be at a proper distance to be recognized as involved in a S-S bond. In your case, if you're certain that there should be a bond, you have to edit the file specbond.dat, find the entry which links two cysteine residues and set the distance to the actual distance in your structure (there is a 10% margin). Hope it helps, Tsjerk On 11/10/06, Giacomo Bastianelli <[EMAIL PROTECTED]> wrote: Dear users, I have just found that gromacs protonate the -S of my Cys and I would like to have it deprotonated to form a disulphide bond (It is present in the original pdb file). Is there any way I can modify it? thanks in advance, Giacomo ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange problem with simple FEP (bug?)
Thanks, but that's indeed not the problem. I'm just doing a PR-run in state A. State B is not of interest in that case. Somehow GROMACS mixes things up internally, I guess. The bugzilla-entry has been placed. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ David Mobley wrote: Maik, I'm trying to do a simple FEP within a simple protein, which seems to make things simple...but as you may expect...it is anything else than that. What I'm trying to do is morphing a Tyrosine into a Phenylalanine in OPLSAA. Therefore the CZ is changed from the type of TYR to the type of PHE. The oxygen(TYR) is changed to a proton(PHE) and the proton(TYR) to a dummy (PHE). So this is very simple. We checked the tpr-dump and everything looks fine (except, maybe, we missed it). Now, in the position-restraint run (where state B should not be regarded by the system), the OH-proton moves on top of the OH-oxygen and the simulation crashes after a while. We then performed a FEP from TYR to TYR (so A- and B-state are the same) and the system runs. I am not an OPLS guy myself, and I don't know the details of your transformation, so I'll just tell you one possibility, and you'll have to decide whether it could apply in your situation. Sometimes, if you are disappearing a Lennard-Jones site that still has some amount of electrostatics, it can begin to interpenetrate with other atoms which either do not have Lennard-Jones interactions (hydrogens in some force fields) or which do (depending on the combination rule you use). Obviously, this is bad because (for example) protons can move on top of oxygens and cause blowing up. A classic example of this is, for example, if I am turning off the LJ on an oxygen site at the same time as turning off the charges on that oxygen. In many FF's, water hydrogens lack LJ interactions, so they can come and overlap with the oxygen I'm disappearing, which is still charged (at least to some degree) and cause a "fusion" type event. I don't know if that's what's going on for you, but you might think about it -- do you have any atoms that you're disappearing, and are there other atoms which the combination rules would allow to overlap with those? The way I get around this problem in my calculations is to always turn off electrostatics on any atom I'm disappearing prior to modifying the LJ parameters, so that I never have a charged atom which is being treated using the "soft-core" potentials that allow overlap. Not sure if that's your problem -- just a thought. David The whole thing was done with GROMACS 3.3.1 and TIP4P. Any suggestions? Gerrit and me think of a bug somewhere. Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Strange problem with simple FEP (bug?)
Update: Checked it with the Amber99 port. Same strange habit. It occured with another protein (system), too. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Maik Goette wrote: Hey all I'm trying to do a simple FEP within a simple protein, which seems to make things simple...but as you may expect...it is anything else than that. What I'm trying to do is morphing a Tyrosine into a Phenylalanine in OPLSAA. Therefore the CZ is changed from the type of TYR to the type of PHE. The oxygen(TYR) is changed to a proton(PHE) and the proton(TYR) to a dummy (PHE). So this is very simple. We checked the tpr-dump and everything looks fine (except, maybe, we missed it). Now, in the position-restraint run (where state B should not be regarded by the system), the OH-proton moves on top of the OH-oxygen and the simulation crashes after a while. We then performed a FEP from TYR to TYR (so A- and B-state are the same) and the system runs. The whole thing was done with GROMACS 3.3.1 and TIP4P. Any suggestions? Gerrit and me think of a bug somewhere. Regards ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Strange problem with simple FEP (bug?)
Hey all I'm trying to do a simple FEP within a simple protein, which seems to make things simple...but as you may expect...it is anything else than that. What I'm trying to do is morphing a Tyrosine into a Phenylalanine in OPLSAA. Therefore the CZ is changed from the type of TYR to the type of PHE. The oxygen(TYR) is changed to a proton(PHE) and the proton(TYR) to a dummy (PHE). So this is very simple. We checked the tpr-dump and everything looks fine (except, maybe, we missed it). Now, in the position-restraint run (where state B should not be regarded by the system), the OH-proton moves on top of the OH-oxygen and the simulation crashes after a while. We then performed a FEP from TYR to TYR (so A- and B-state are the same) and the system runs. The whole thing was done with GROMACS 3.3.1 and TIP4P. Any suggestions? Gerrit and me think of a bug somewhere. Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Possible Bug GROMACS 3.3.1 - NMA
Yes, I'm using Cut-off. And the Error is reproducable. I'll post the bug report. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ David van der Spoel wrote: Maik Goette wrote: Hi I just observed very strange results with my system (around 700 atoms in vacuum), when doing normal mode analysis. The eigenvalues were all negative. I then took an old nma-system from Bert de Groot and did the nma with 3.3.1 on it and observed the same strange results. After that I tried 3.2.1 on that system and the results were quite similar to the ones Bert got with 3.1.4. My vacuum-system yields (more or less) correct (not nice) results on the first look. Is there something new to obey in 3.3.1 what isn't mentioned in the manual (3.11 NMA)? If not, I would think, there's a bug. Any suggestions? Regards Are you using cut-offs? In that case gromacs uses a different algorithm now, which might cause the problem. Anyway if you have a reproducible problem please report a bugzilla and upload the necessary files. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Possible Bug GROMACS 3.3.1 - NMA
Hi I just observed very strange results with my system (around 700 atoms in vacuum), when doing normal mode analysis. The eigenvalues were all negative. I then took an old nma-system from Bert de Groot and did the nma with 3.3.1 on it and observed the same strange results. After that I tried 3.2.1 on that system and the results were quite similar to the ones Bert got with 3.1.4. My vacuum-system yields (more or less) correct (not nice) results on the first look. Is there something new to obey in 3.3.1 what isn't mentioned in the manual (3.11 NMA)? If not, I would think, there's a bug. Any suggestions? Regards -- Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
