Re: [gmx-users] Fatal error: Atomtype F not found
On 2012-10-04 04:39, Nur Syafiqah Abdul Ghani wrote: Dear Users, Right now i already done for creating the a gro file from antechamber to gromacs format of my molecule which is hexafluoroisopropanol. But when i want to minimize it in vacuum it show atomtype F not found. Im using oplsaa force field and i already change the atom type according to the force field. Do not combine force fields. Use antechamber and the gromacs conversion script to make a gromacs topology from it (amb2gmx.pl, search on google), then use amber force field in combination with this if you want to dissolve biomolecules or something like that. More organic molecules topologies can be found at http://virtualchemistry.org -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] can we generate .xtc file directly from mdrun?
hello: I found that the .trr from mdrun output is really much huger than the .xtc file. However, most people would like to generate the .trr file and then convert it into .xtc file. I am just wondering can we generate the .xtc file directly from mdrun command like: mdrun -s md.tpr -o md.xtc I also found that the CHARMM36 FF (charmm36.ff_4.5.4_ref.tgz http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz) in gromac website seems to be update, I am wondering is it the latest CHARMM37 FF? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coordinate file for lipid bilayer
To generate starting (non-equilibrated) bilayer structures for use in MD simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/. Otherwise, for conventional lipids CHARMM-GUI membrane builder (http://www.charmm-gui.org/?doc=input/membrane). Hope it helps! Felipe On 10/04/2012 07:46 AM, James Starlight wrote: Justin, lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). My advice is still the same - you need box vectors that are compatible with both a sensible water layer and membrane leaflets. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] can we generate .xtc file directly from mdrun?
On 10/04/2012 09:22 AM, rama david wrote: Yes -x option ( please see mdrun -h ) You have to specify it as the output is optiona l if you use -deffnm all the output posses the same name ( generally I do these one ) set the mdp file option properly to get appropriate saving for xtc ( see the manual for these one ) Hi thanks for kind comments. here is what I found http://manual.gromacs.org/current/online/mdp_opt.html#out shall I simple turn on the nsxtcout and xtc_precision option on like: ; Parameters controlling output writing nstxout= 5000; Write coordinates to output file nstvout= 5000; Write velocities to output file nstenergy= 1000; Write energies to output .edr file nstlog= 1000; Write output to .log file nsxtcout = 5000 xtc_precision = 1000 THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
AW: [gmx-users] can we generate .xtc file directly from mdrun?
Hello Albert, Yes, the settings you mentioned will give you .trr and .xtc files during mdrun. But please watch out, you have a little spelling typo in your message. It is nstxtcout. Cheers, Felix -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von Albert Gesendet: Donnerstag, 4. Oktober 2012 09:45 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] can we generate .xtc file directly from mdrun? On 10/04/2012 09:22 AM, rama david wrote: Yes -x option ( please see mdrun -h ) You have to specify it as the output is optiona l if you use -deffnm all the output posses the same name ( generally I do these one ) set the mdp file option properly to get appropriate saving for xtc ( see the manual for these one ) Hi thanks for kind comments. here is what I found http://manual.gromacs.org/current/online/mdp_opt.html#out shall I simple turn on the nsxtcout and xtc_precision option on like: ; Parameters controlling output writing nstxout= 5000; Write coordinates to output file nstvout= 5000; Write velocities to output file nstenergy= 1000; Write energies to output .edr file nstlog= 1000; Write output to .log file nsxtcout = 5000 xtc_precision = 1000 THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] can we generate .xtc file directly from mdrun?
On 4/10/2012 5:10 PM, Albert wrote: hello: I found that the .trr from mdrun output is really much huger than the .xtc file. However, most people would like to generate the .trr file and then convert it into .xtc file. See http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume Mark I am just wondering can we generate the .xtc file directly from mdrun command like: mdrun -s md.tpr -o md.xtc I also found that the CHARMM36 FF (charmm36.ff_4.5.4_ref.tgz http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz) in gromac website seems to be update, I am wondering is it the latest CHARMM37 FF? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault, mdrun_mpi
So I have spent the past few weeks debugging my equilibration protocols, which were an odd hybrid of examples ranging from GROMACS 3.3 up to GROMACS 4.5. I have cleaned out old code. I added an in vacuo energy minimization step for the protein without solvent, and a missing NVT step after solvent is defined. I have dimly grasped that, as long as you don't require compatibility with an older simulation, the V-rescale thermostat is the current recommended choice, and that switching thermostats (unlike barostats) can cause instabilities. I now know how to examine and graph macroscopic system parameters to assess stability. I think that everything should be looking good right now -- except that it isn't, not quite. When I finally start the production MD runs, I have received two segmentation faults on two different test structures. They take a LONG time to appear -- over 1,070,000 iterations on one run, and over 2,360,000 iterations on another. On top of that, I'm not getting my usual error messages -- PME errors, or SETTLE errors. I'm not getting a dump of the last frame of my simulation. I had enough trouble accepting that my simulation parameters were set up incorrectly when I had failures 100,000 steps after starting the production MD run. Am I really supposed to believe that I still have instability problems? Here is the terminal output from one run (executing mdrun_mpi): Reading file test-prep.tpr, VERSION 4.5.4 (single precision) Making 1D domain decomposition 5 x 1 x 1 starting mdrun 'Protein t= 0.0 in water' 250 steps, 5000.0 ps. [john-linux:09596] *** Process received signal *** [john-linux:09596] Signal: Segmentation fault (11) [john-linux:09596] Signal code: Address not mapped (1) [john-linux:09596] Failing at address: 0x3e950840 [john-linux:09596] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10060) [0x7f8a8ad5c060] [john-linux:09596] [ 1] /usr/lib/libgmx_mpi.openmpi.so.6(+0x1f9670) [0x7f8a8b413670] [john-linux:09596] *** End of error message *** -- mpirun noticed that process rank 2 with PID 9596 on node john-linux exited on signal 11 (Segmentation fault). -- The .log file does NOT contain any error messages, indicating any instability. The last entry in the log file is a long chain of energy status report blocks. Here's the last one: DD step 1078799 load imb.: force 1.8% Step Time Lambda 1078800 2157.60.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.07623e+038.42439e+026.03967e+02 -2.12322e+021.95589e+04 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 8.12766e+04 -9.12661e+02 -5.96406e+05 -4.40546e+04 -5.37227e+05 Kinetic En. Total EnergyTemperature Pres. DC (bar) Pressure (bar) 9.76293e+04 -4.39598e+053.10969e+02 -7.72781e+013.95185e+01 Constr. rmsd 1.90839e-05 I'm not a low-level programmer, and so I don't have to deal with this much, but... a segmentation fault generally indicates that a program is trying to write outside of its allocated memory block. The third line of the error message sent to the shell would seem to indicate exactly that. That doesn't actually sound like it has anything to do with my simulation being unstable. (However, with applications written in C, I'm willing to believe anything.) I did check on my memory usage. I have 8 GB of RAM on my system, running Ubuntu Linux 11.10, AMD 64-bit. At most, I'm using a bit more than half of my RAM (I have other, undemanding applications open besides my GROMACS terminal windows, and I also reserved one CPU core to run those apps). I think that I should be fine. If they would help, I can repost my cleaned-up MDP files. I can post graphs of potential, pressure, temperature, density, etc., from any phase in my protocol. Or you could just take my word for it that all of these parameters converge nicely during my equilibration procedure, and then remain stable throughout the production MD run. My target temperature is 310 K (37 C), and I get very close to that value on average. My average pressure and density readings are both a bit lower than my targets (0.80 bar and 988 kg/m^3, respectively), but they are consistent. I have examined a series of snapshots of my protein. It isn't undergoing any radical movements. My systems are on the small side, under 50,000 atoms. It's all amino acids and water molecules. Puzzled once again. Thanks for your advice! -- View this message in context: http://gromacs.5086.n6.nabble.com/Segmentation-fault-mdrun-mpi-tp5001601.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please
Re: [gmx-users] Dssp core dumped
Hi Rama, I bet that wasn't the only output you got. Two things can usually happen with do_dssp. Either you chose the wrong group for analysis, or there is a problem with the version of DSSP. Probably the latter: DSSP syntax changed recently, and I think that GMX 4.5.5 can't deal with that. There should be capital punishment on syntax changes on such programs... Try digging up an older version of DSSP. Cheers, Tsjerk On Thu, Oct 4, 2012 at 11:18 AM, rama david ramadavidgr...@gmail.com wrote: hi Gromacs Friend i Install dssp 2.0.4 . I am using gromacs 4.5.5 I put dssp in /usr/local/bin I try with export DSSP=/usr/local/bin/dssp When Run dssp with simple pdb file it run but when I run do_dssp command i got following output.. Segmentation fault (core dumped) (dssp -h DSSP 2.0.4 options: -h [ --help ] Display help message ) I also goes through archive but not find out the answer. Please tel me how to figure out these problem With best wishes and regards.. rama david -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)
Dear all, I am using the pull code in Gromacs 4.5.5 to constrain the distance in one direction (z) between a small molecule and a lipid bilayer. I run separate simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder. The pull parameters are the following: pull = constraint pull_geometry = cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DMPC pull_group1 = 2 pull_vec1 = 0 0 1 pull_init1 = x I have previously been using the same methodology in 4.0.5 without problems. When i run grompp in 4.5.5 I get the following error: Fatal error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310) The source of the first value, which should be the distance of pull group 1 is for me unknown. A value of ~4 is generated for all systems no matter what z distance is actually betwen the two groups (0-4 nm), so the value has no connection to the z distance between the groups. The second value is 0.5 times the x box length. I have read through pull.c, but I cannot find an explanation to why the x direction seems to be considered and not the z direction. When I run grompp with pull_geometry = distance or direction together with pull_dim = N N Y there is no problem. As I am not sure of the source of this error when running with cylinder I do not know if it is only related to the check or if the following simulation would be affected if I uncomment the check. Any suggestions to why this is happening and what I can do about it? Thanks! Best regards, Emma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction study for peptide-receptor..
On 10/4/12 2:01 AM, rama david wrote: Hi gromacs Friends, I want to do peptide-receptor ( Protein) interaction study.Receptor consist a single chain. Peptide is made up of 4 amino acids. I know the interaction pattern of peptide and receptor. I plan to mutate single residue each at a time and run 4 simulation . So I will have the 4 different simulation that contain the mutated residues and the wild one. Then afterward from the interaction energy I want to select the peptide which is showing stronger interaction than others. As mention I know the binding site, If I freeze the remaining portion in receptor that not involved in binding , Is it going to affect my screening process ??? Potentially. Do you know that the binding interactions and the mutations will only perturb local residues? Do you know that there are no long-range motions to be considered? I think you gain very little by freezing portions of the system, and risk more than you gain. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction study for peptide-receptor..
thank you Justin for reply. I dont know about long range interactions. But as I freeze the group I think it will improve my computational speed. So is there any way to find out or decide which group should be freeze, and which group should affect my interaction most probably?? Should I do Essential Dynamics ??? or Principle component analysis ??? Would you suggest me any general protocol for such work?? Thank you in Advance With Best Wishes and regards. Rama David On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/4/12 2:01 AM, rama david wrote: Hi gromacs Friends, I want to do peptide-receptor ( Protein) interaction study.Receptor consist a single chain. Peptide is made up of 4 amino acids. I know the interaction pattern of peptide and receptor. I plan to mutate single residue each at a time and run 4 simulation . So I will have the 4 different simulation that contain the mutated residues and the wild one. Then afterward from the interaction energy I want to select the peptide which is showing stronger interaction than others. As mention I know the binding site, If I freeze the remaining portion in receptor that not involved in binding , Is it going to affect my screening process ??? Potentially. Do you know that the binding interactions and the mutations will only perturb local residues? Do you know that there are no long-range motions to be considered? I think you gain very little by freezing portions of the system, and risk more than you gain. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction study for peptide-receptor..
Hi, as far as I know, freezing just set velocities to 0 so you gain nothing freezing atoms. By the way, have you tried docking? It takes into account multiple conformation and orientation of the peptide and, depending upon the implemented algorithm, also protein sidechain orientation. Francesco 2012/10/4 rama david ramadavidgr...@gmail.com thank you Justin for reply. I dont know about long range interactions. But as I freeze the group I think it will improve my computational speed. So is there any way to find out or decide which group should be freeze, and which group should affect my interaction most probably?? Should I do Essential Dynamics ??? or Principle component analysis ??? Would you suggest me any general protocol for such work?? Thank you in Advance With Best Wishes and regards. Rama David On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/4/12 2:01 AM, rama david wrote: Hi gromacs Friends, I want to do peptide-receptor ( Protein) interaction study.Receptor consist a single chain. Peptide is made up of 4 amino acids. I know the interaction pattern of peptide and receptor. I plan to mutate single residue each at a time and run 4 simulation . So I will have the 4 different simulation that contain the mutated residues and the wild one. Then afterward from the interaction energy I want to select the peptide which is showing stronger interaction than others. As mention I know the binding site, If I freeze the remaining portion in receptor that not involved in binding , Is it going to affect my screening process ??? Potentially. Do you know that the binding interactions and the mutations will only perturb local residues? Do you know that there are no long-range motions to be considered? I think you gain very little by freezing portions of the system, and risk more than you gain. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction study for peptide-receptor..
Hi francesco, Thank you For reply. I did docking but the result are not so impressive. I used vina and autodock. I also did virtual screening in autodock but the result are not upto the mark. Is the freezing of group can affect my system?? How much efficiency I get by these work?? As these group are going to freeze in four simulation so if it affect one ligand it affect other ligand also. I read article that did the work like me , they sliced the binding residues and used the inert solid sphere to support binding residues instead of the freezing group other group. I think both way should have same effect..Am I right or wrong?? If you have any other way please suggest it.. With best wishes and regards Rama david On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi, as far as I know, freezing just set velocities to 0 so you gain nothing freezing atoms. By the way, have you tried docking? It takes into account multiple conformation and orientation of the peptide and, depending upon the implemented algorithm, also protein sidechain orientation. Francesco 2012/10/4 rama david ramadavidgr...@gmail.com thank you Justin for reply. I dont know about long range interactions. But as I freeze the group I think it will improve my computational speed. So is there any way to find out or decide which group should be freeze, and which group should affect my interaction most probably?? Should I do Essential Dynamics ??? or Principle component analysis ??? Would you suggest me any general protocol for such work?? Thank you in Advance With Best Wishes and regards. Rama David On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/4/12 2:01 AM, rama david wrote: Hi gromacs Friends, I want to do peptide-receptor ( Protein) interaction study.Receptor consist a single chain. Peptide is made up of 4 amino acids. I know the interaction pattern of peptide and receptor. I plan to mutate single residue each at a time and run 4 simulation . So I will have the 4 different simulation that contain the mutated residues and the wild one. Then afterward from the interaction energy I want to select the peptide which is showing stronger interaction than others. As mention I know the binding site, If I freeze the remaining portion in receptor that not involved in binding , Is it going to affect my screening process ??? Potentially. Do you know that the binding interactions and the mutations will only perturb local residues? Do you know that there are no long-range motions to be considered? I think you gain very little by freezing portions of the system, and risk more than you gain. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
Re: [gmx-users] Interaction study for peptide-receptor..
On 10/4/12 8:08 AM, rama david wrote: Hi francesco, Thank you For reply. I did docking but the result are not so impressive. I used vina and autodock. I also did virtual screening in autodock but the result are not upto the mark. Is the freezing of group can affect my system?? How much efficiency I get by these work?? You will not get any improvement in computational efficiency, and if you use NPT, you will get artifacts. One can potentially speed up a calculation using energygrp_excl, but that's layering assumptions upon assumptions, which I think is bad news. You've said you don't know if long-range interactions play a role. That, to me, means you absolutely cannot justify any sort of freezing. The fact that docking did not produce very good results is unsurprising. The largely rigid treatment of proteins in docking leaves much to be desired. This is yet another argument against freezing parts of your protein - if docking did not produce good results, why would you expect a mostly frozen MD system to perform much better? As these group are going to freeze in four simulation so if it affect one ligand it affect other ligand also. I read article that did the work like me , they sliced the binding residues and used the inert solid sphere to support binding residues instead of the freezing group other group. I think both way should have same effect..Am I right or wrong?? I don't really understand what it is the other group did, aside from perhaps modeling a subsystem. Still, I don't think such lengths are necessary or inherently beneficial. If you have any other way please suggest it.. I see no reason not to treat this system with normal MD protocols. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction study for peptide-receptor..
2012/10/4 rama david ramadavidgr...@gmail.com Hi francesco, Thank you For reply. I did docking but the result are not so impressive. What does it mean not so impressive? I mean, do you have experimental data and the comparison with docking doesn't agree with experiments? Have you generated a sufficient number of complexes (say 100 or more)? I used vina and autodock. I also did virtual screening in autodock but the result are not upto the mark. Is the freezing of group can affect my system?? How much efficiency I get by these work?? It will change a lot the dynamics of your system and I don't think calculations will be more efficient! As these group are going to freeze in four simulation so if it affect one ligand it affect other ligand also. I read article that did the work like me , they sliced the binding residues and used the inert solid sphere to support binding residues instead of the freezing group other group. I think both way should have same effect..Am I right or wrong?? If you have any other way please suggest it.. If you already have docking complexes, you can pick up one complex for each peptide, to run an MD, or Free Energy calculations. It strongly depends by the experimentale data you have and what is the target of your work. With best wishes and regards Rama david On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi, as far as I know, freezing just set velocities to 0 so you gain nothing freezing atoms. By the way, have you tried docking? It takes into account multiple conformation and orientation of the peptide and, depending upon the implemented algorithm, also protein sidechain orientation. Francesco 2012/10/4 rama david ramadavidgr...@gmail.com thank you Justin for reply. I dont know about long range interactions. But as I freeze the group I think it will improve my computational speed. So is there any way to find out or decide which group should be freeze, and which group should affect my interaction most probably?? Should I do Essential Dynamics ??? or Principle component analysis ??? Would you suggest me any general protocol for such work?? Thank you in Advance With Best Wishes and regards. Rama David On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/4/12 2:01 AM, rama david wrote: Hi gromacs Friends, I want to do peptide-receptor ( Protein) interaction study.Receptor consist a single chain. Peptide is made up of 4 amino acids. I know the interaction pattern of peptide and receptor. I plan to mutate single residue each at a time and run 4 simulation . So I will have the 4 different simulation that contain the mutated residues and the wild one. Then afterward from the interaction energy I want to select the peptide which is showing stronger interaction than others. As mention I know the binding site, If I freeze the remaining portion in receptor that not involved in binding , Is it going to affect my screening process ??? Potentially. Do you know that the binding interactions and the mutations will only perturb local residues? Do you know that there are no long-range motions to be considered? I think you gain very little by freezing portions of the system, and risk more than you gain. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users
Re: [gmx-users] Re: Fatal error: Atomtype F not found
On 10/3/12 11:41 PM, shika wrote: Thanks for fast reply.I am very new to this and yes I am confused my itp file is : ; solvent_HFI.gro.top created by rdparm2gmx.pl Sat May 28 10:25:18 MYT 2005 ; ; [ moleculetype ] ; Namenrexcl solute 3 [ atoms ] ; nr type resnr residue atomcgnr charge mass typeBchargeB 1 opls_164 1 HFI F 1 -0.234745 19.00 2 opls_161 1 HFI C 2 0.705532 12.00 3 opls_164 1 HFI F1 3 -0.205102 19.00 4 opls_164 1 HFI F2 4 -0.237125 19.00 5 opls_158 1 HFI C1 5 -0.119035 12.00 6 opls_078 1 HFI O 6 -0.600958 16.00 7 opls_079 1 HFI H1 7 0.468121 1.00 8 opls_140 1 HFI H 8 0.141115 1.00 9 opls_161 1 HFI C2 9 0.786317 12.00 10 opls_164 1 HFI F4 10 -0.230854 19.00 11 opls_164 1 HFI F5 11 -0.266972 19.00 12 opls_164 1 HFI F3 12 -0.206295 19.00 [ bonds ] ; aiaj funct 5 8 1 6 7 1 1 2 1 2 3 1 2 4 1 2 5 1 5 6 1 5 9 1 910 1 911 1 912 1 [ pairs ] ; aiaj funct 1 8 1 2 7 1 3 8 1 4 8 1 7 8 1 7 9 1 8 10 1 8 11 1 8 12 1 1 6 1 1 9 1 2 10 1 2 11 1 2 12 1 3 6 1 3 9 1 4 6 1 4 9 1 6 10 1 6 11 1 6 12 1 [ angles ] ; aiajak funct 2 5 8 1 5 6 7 1 6 5 8 1 8 5 9 1 1 2 3 1 1 2 4 1 1 2 5 1 2 5 6 1 2 5 9 1 3 2 4 1 3 2 5 1 4 2 5 1 5 910 1 5 911 1 5 912 1 6 5 9 1 10 911 1 10 912 1 11 912 1 [ dihedrals ] ;i j k l func 1258 3 2567 3 3258 3 4258 3 7658 3 7659 3 85910 3 85911 3 85912 3 1256 3 1259 3 25910 3 25911 3 25912 3 3256 3 3259 3 4256 3 4259 3 65910 3 65911 3 65912 3 I would be grateful if you could highlight things that need to be edited. There is no atomtype F referenced in this topology, so the source of the error is still unclear. One more thing,is OPLSAA forcefield suitable for my non standard molecule? Any force field can be used for any molecule, provided the parameterization was done thoroughly and evaluated properly. The header of your topology suggests you used an AMBER conversion script, so you may be mixing and matching parameters here, which is a bad idea. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] hexafluoroisopropanol
On 10/4/12 1:34 AM, Nur Syafiqah Abdul Ghani wrote: Hi Guys, Need your help urgently. I already read a lot of paper about molecular dynamics simulation which relate work as mine.The main point is to create the mix solvent. The co-solvent is hexafluoroisopropanol and a lot of researcher cited the journal name 1,1,1,3,3,3-hexafluoro-propan-2-ol for molecular dynamics simulations by Fioroni. So my question,is the molecule already have a pdb structure?Have anyone dealing with this compound? Constructing a coordinate file for a small organic molecule is rather simple with any number of tools. http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources Because im currently lost due to my HFIP pdb is wrong and the atom type of F is not recognized and the force field i used is OPLSAA but right now i think i need to change it to the GROMOS96..Your advise are highly appreciate.. You should not presume that one force field is inherently better than another for an arbitrary molecule that is not already parameterized. One could produce reliable parameters for any force field, provided care is taken to derive and evaluate them properly. There seem to be two threads with nearly identical problems. Perhaps you can cross-reference some information with the other active thread. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction study for peptide-receptor..
Thank you justin and franscisco, I have practical data that claim that only a particular residue that is c terminal residue is involve in binding. but when I generate the docking data other residues most of the time comes to play. I know the binding of natural ligand ( peptide ) and the position. so I think if I mutate only these residue and simulate the system I will get the structure that is more active. In natural ligand the C terminal is playing important role. With simulation i will find interaction energy. That will tell me about binding affinity ( Hope so ) These is my basic idea. Is any other way to do the same thing.. With best wishes and regards Rama David On Thu, Oct 4, 2012 at 5:47 PM, francesco oteri francesco.ot...@gmail.comwrote: 2012/10/4 rama david ramadavidgr...@gmail.com Hi francesco, Thank you For reply. I did docking but the result are not so impressive. What does it mean not so impressive? I mean, do you have experimental data and the comparison with docking doesn't agree with experiments? Have you generated a sufficient number of complexes (say 100 or more)? I used vina and autodock. I also did virtual screening in autodock but the result are not upto the mark. Is the freezing of group can affect my system?? How much efficiency I get by these work?? It will change a lot the dynamics of your system and I don't think calculations will be more efficient! As these group are going to freeze in four simulation so if it affect one ligand it affect other ligand also. I read article that did the work like me , they sliced the binding residues and used the inert solid sphere to support binding residues instead of the freezing group other group. I think both way should have same effect..Am I right or wrong?? If you have any other way please suggest it.. If you already have docking complexes, you can pick up one complex for each peptide, to run an MD, or Free Energy calculations. It strongly depends by the experimentale data you have and what is the target of your work. With best wishes and regards Rama david On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi, as far as I know, freezing just set velocities to 0 so you gain nothing freezing atoms. By the way, have you tried docking? It takes into account multiple conformation and orientation of the peptide and, depending upon the implemented algorithm, also protein sidechain orientation. Francesco 2012/10/4 rama david ramadavidgr...@gmail.com thank you Justin for reply. I dont know about long range interactions. But as I freeze the group I think it will improve my computational speed. So is there any way to find out or decide which group should be freeze, and which group should affect my interaction most probably?? Should I do Essential Dynamics ??? or Principle component analysis ??? Would you suggest me any general protocol for such work?? Thank you in Advance With Best Wishes and regards. Rama David On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/4/12 2:01 AM, rama david wrote: Hi gromacs Friends, I want to do peptide-receptor ( Protein) interaction study.Receptor consist a single chain. Peptide is made up of 4 amino acids. I know the interaction pattern of peptide and receptor. I plan to mutate single residue each at a time and run 4 simulation . So I will have the 4 different simulation that contain the mutated residues and the wild one. Then afterward from the interaction energy I want to select the peptide which is showing stronger interaction than others. As mention I know the binding site, If I freeze the remaining portion in receptor that not involved in binding , Is it going to affect my screening process ??? Potentially. Do you know that the binding interactions and the mutations will only perturb local residues? Do you know that there are no long-range motions to be considered? I think you gain very little by freezing portions of the system, and risk more than you gain. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users
Re: [gmx-users] Interaction study for peptide-receptor..
On 10/4/12 8:40 AM, rama david wrote: Thank you justin and franscisco, I have practical data that claim that only a particular residue that is c terminal residue is involve in binding. but when I generate the docking data other residues most of the time comes to play. I know the binding of natural ligand ( peptide ) and the position. so I think if I mutate only these residue and simulate the system I will get the structure that is more active. In natural ligand the C terminal is playing important role. With simulation i will find interaction energy. Interaction energy is a very vague term that people often use fairly erroneously to justify their findings. Force fields are not necessarily guaranteed to produce anything meaningful from the sum of nonbonded terms. That will tell me about binding affinity ( Hope so ) More sophisticated free energy calculations would be necessary to determine binding affinity or free energy of binding. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction study for peptide-receptor..
I don't think AutoDock and Vina are suitable for peptide docking. I would first try the FlexPepDocking module of Rosetta which does ab initio folding of the peptide on the receptor, while moving the side-chains of the protein but leaves its backbone intact. Rosetta implements a knowledge-based scoring, which has been specifically designed for this task and is as fast as Vina or AutoDock. I would first do that and if I wouldn't get any reasonable results then I would move to MD starting from the top scored protein-peptide complexes created by Rosetta. Thomas On 4 October 2012 15:08, rama david ramadavidgr...@gmail.com wrote: Hi francesco, Thank you For reply. I did docking but the result are not so impressive. I used vina and autodock. I also did virtual screening in autodock but the result are not upto the mark. Is the freezing of group can affect my system?? How much efficiency I get by these work?? As these group are going to freeze in four simulation so if it affect one ligand it affect other ligand also. I read article that did the work like me , they sliced the binding residues and used the inert solid sphere to support binding residues instead of the freezing group other group. I think both way should have same effect..Am I right or wrong?? If you have any other way please suggest it.. With best wishes and regards Rama david On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi, as far as I know, freezing just set velocities to 0 so you gain nothing freezing atoms. By the way, have you tried docking? It takes into account multiple conformation and orientation of the peptide and, depending upon the implemented algorithm, also protein sidechain orientation. Francesco 2012/10/4 rama david ramadavidgr...@gmail.com thank you Justin for reply. I dont know about long range interactions. But as I freeze the group I think it will improve my computational speed. So is there any way to find out or decide which group should be freeze, and which group should affect my interaction most probably?? Should I do Essential Dynamics ??? or Principle component analysis ??? Would you suggest me any general protocol for such work?? Thank you in Advance With Best Wishes and regards. Rama David On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/4/12 2:01 AM, rama david wrote: Hi gromacs Friends, I want to do peptide-receptor ( Protein) interaction study.Receptor consist a single chain. Peptide is made up of 4 amino acids. I know the interaction pattern of peptide and receptor. I plan to mutate single residue each at a time and run 4 simulation . So I will have the 4 different simulation that contain the mutated residues and the wild one. Then afterward from the interaction energy I want to select the peptide which is showing stronger interaction than others. As mention I know the binding site, If I freeze the remaining portion in receptor that not involved in binding , Is it going to affect my screening process ??? Potentially. Do you know that the binding interactions and the mutations will only perturb local residues? Do you know that there are no long-range motions to be considered? I think you gain very little by freezing portions of the system, and risk more than you gain. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali
Re: [gmx-users] Coordinate file for lipid bilayer
Dear Felipe, thanks for advise. Does the Packmol software suitable for generation coordinates of the bergers ( for gromos 56 ff) lipids ? As I know CHARMM-GUI membrane builder is suitable for only CHARMM force field lipids. James 2012/10/4 Felipe Pineda, PhD luis.pinedadecas...@lnu.se: To generate starting (non-equilibrated) bilayer structures for use in MD simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/. Otherwise, for conventional lipids CHARMM-GUI membrane builder (http://www.charmm-gui.org/?doc=input/membrane). Hope it helps! Felipe On 10/04/2012 07:46 AM, James Starlight wrote: Justin, lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). My advice is still the same - you need box vectors that are compatible with both a sensible water layer and membrane leaflets. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Coordinate file for lipid bilayer
Hi, packmol generates just coordinates (pdb format) for optimized packing arrangements of whatever molecule you provide as input. It's up to you to parameterize the resulting model. CHARMM-GUI has a library of conventional (phospho)lipids and generates the input for CHARMM equilibration of the bilayer model built with those lipids. But, you should inspect by yourself the corresponding sites. Felipe On 10/04/2012 03:11 PM, James Starlight wrote: Dear Felipe, thanks for advise. Does the Packmol software suitable for generation coordinates of the bergers ( for gromos 56 ff) lipids ? As I know CHARMM-GUI membrane builder is suitable for only CHARMM force field lipids. James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction study for peptide-receptor..
Thank you for reply, I read the recently published article in Biochemistry. They worked on the same receptor that I am working. ( as I mention in my previous mail) They used NAMD software and I am using gromacs. They sliced the receptor binding site and used the the solid support to the binding site and did simulation. So if I freeze the group is it will ok ?? Is it possible in gromacs to fix the residue on solid immobilized surface. If it is how to do it?? my question is How to decide which group are remove and which group should keep in simulation. thank you in advance Thank you for giving your valuable time and advice to me. With best wishes and regards, Rama david On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis teva...@gmail.comwrote: I don't think AutoDock and Vina are suitable for peptide docking. I would first try the FlexPepDocking module of Rosetta which does ab initio folding of the peptide on the receptor, while moving the side-chains of the protein but leaves its backbone intact. Rosetta implements a knowledge-based scoring, which has been specifically designed for this task and is as fast as Vina or AutoDock. I would first do that and if I wouldn't get any reasonable results then I would move to MD starting from the top scored protein-peptide complexes created by Rosetta. Thomas On 4 October 2012 15:08, rama david ramadavidgr...@gmail.com wrote: Hi francesco, Thank you For reply. I did docking but the result are not so impressive. I used vina and autodock. I also did virtual screening in autodock but the result are not upto the mark. Is the freezing of group can affect my system?? How much efficiency I get by these work?? As these group are going to freeze in four simulation so if it affect one ligand it affect other ligand also. I read article that did the work like me , they sliced the binding residues and used the inert solid sphere to support binding residues instead of the freezing group other group. I think both way should have same effect..Am I right or wrong?? If you have any other way please suggest it.. With best wishes and regards Rama david On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi, as far as I know, freezing just set velocities to 0 so you gain nothing freezing atoms. By the way, have you tried docking? It takes into account multiple conformation and orientation of the peptide and, depending upon the implemented algorithm, also protein sidechain orientation. Francesco 2012/10/4 rama david ramadavidgr...@gmail.com thank you Justin for reply. I dont know about long range interactions. But as I freeze the group I think it will improve my computational speed. So is there any way to find out or decide which group should be freeze, and which group should affect my interaction most probably?? Should I do Essential Dynamics ??? or Principle component analysis ??? Would you suggest me any general protocol for such work?? Thank you in Advance With Best Wishes and regards. Rama David On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/4/12 2:01 AM, rama david wrote: Hi gromacs Friends, I want to do peptide-receptor ( Protein) interaction study.Receptor consist a single chain. Peptide is made up of 4 amino acids. I know the interaction pattern of peptide and receptor. I plan to mutate single residue each at a time and run 4 simulation . So I will have the 4 different simulation that contain the mutated residues and the wild one. Then afterward from the interaction energy I want to select the peptide which is showing stronger interaction than others. As mention I know the binding site, If I freeze the remaining portion in receptor that not involved in binding , Is it going to affect my screening process ??? Potentially. Do you know that the binding interactions and the mutations will only perturb local residues? Do you know that there are no long-range motions to be considered? I think you gain very little by freezing portions of the system, and risk more than you gain. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] Coordinate file for lipid bilayer
Hi James, The bilayers from the CHARMM-GUI can be converted into any force field using a simple script. For a united-atom force field you will need to remove the non-polar hydrogens, rename the atoms and possibly reorder some of the atoms in the lipids. As for other methods to build membranes, there are numerous different methods available. One of the simplest approaches is to use genconf to replicate a single lipid up to the desired size of membrane and perform and simulation to equilibrate the properties of your membrane (although depending upon the lipid and force field this may require simulations in the order of several hundreds of ns though). Another fairly simple method (which can also be easily used to make hexagonal membranes) is to self-assemble a coarse-grained membrane, map that back to an atomistic representation (using one of a number of available tools) and equilibrate. One issue using this method is that the self-assembly often results in uneven numbers of lipids per membrane leaflet. This, however, is easy to correct after the self-assembly. Cheers Tom James Starlight wrote: Dear Felipe, thanks for advise. Does the Packmol software suitable for generation coordinates of the bergers ( for gromos 56 ff) lipids ? As I know CHARMM-GUI membrane builder is suitable for only CHARMM force field lipids. James 2012/10/4 Felipe Pineda, PhD luis.pinedadecas...@lnu.se: To generate starting (non-equilibrated) bilayer structures for use in MD simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/. Otherwise, for conventional lipids CHARMM-GUI membrane builder (http://www.charmm-gui.org/?doc=input/membrane). Hope it helps! Felipe On 10/04/2012 07:46 AM, James Starlight wrote: Justin, lastly, is there any other ways to obtain bilayers of desired dimensions started from just one lipid oriented in desired way for instance? James 2012/10/3, Justin Lemkul jalem...@vt.edu: On 10/3/12 12:38 PM, James Starlight wrote: Justin, thanks for advises. Finally how I could effectively reduce size of my system (in x and y ) to the defined pbc box size ( see picture to the previous comment) ? I've noticed that increasing of x and y to the 12 nm I obtain ideal shape of the bilayer without miss-matches of the left and right sizes. But when I try to decrease dimensions of that system from 12 to 8 nm genbox -cs xz.gro -box 8.04542 8.04542 10.19156 I've obtained the system with the broadered water layers again ( as in the picture which I've shown). My advice is still the same - you need box vectors that are compatible with both a sensible water layer and membrane leaflets. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] equilibrium for box of simulation
Dear GROMACS Users, I asked this question before but I don't understand it! I placed several materials in my box of simulation for example box with 6nm*6nm*6nm and my materials are not placed in the smaller box but when I equilibrate my system, the box became smaller and temperature and pressure also equilibrate. my question is: is my system and equilibrate mistake, because of reach to smaller box? Is there equilibriums with reach to smaller box? I thanks from you for help to me. Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Hello everyone, Justin, I have repeated the procedures without doing any changes and it does seem that you were right about the broken file. However now I get a different set of errors: (1) ERROR 1 [file ffoplsaabon.itp, line 2692]: Incorrect number of atomtypes for dihedral (4 instead of 2 or 4) (2) ERROR 2 [file ffoplsaabon.itp, line 2694]: Not enough parameters and then a lot of errors of the type: ERROR 3 [file S54.top, line 118]: No default Bond types ERROR 4 [file S54.top, line 120]: No default Bond types ERROR 5 [file S54.top, line 124]: No default Bond types ERROR 6 [file S54.top, line 127]: No default Bond types... Maybe the main question is for the third error is how to define these bond types and angles? Thank you. Elie Date: Wed, 3 Oct 2012 22:09:02 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/3/12 7:48 PM, Elie M wrote: Sorry it seems that those breaks are due to hotmail and not present in the topology. Thanks for your reply. I still have problems...I will tell u briefly and as clear as possible what i did. (1) My top file has the following lines ate first: ; Include forcefield parameters #include ffoplsaamod.itp[ moleculetype ] which means that when grompp is reading it, it will first go to ffoplsaamod.itp. (2) After the description of what the ffoplsaamod is (commented by ;), the input is simply: [ defaults ];nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 3 yes 0.5 0.5 #include ffoplsaanb.itp#include ffoplsaabon.itp where the nonbonded and bonded parameters are included in this order (which you have also mentioned in your previous e-mail). If i run grompp in this way I get the error: Fatal error:Syntax error - File ffoplsaamod.itp, line 18Last line read:'\par'Found a second defaults directive. which I really cannot understand. The above [defaults] is the first thing that the code will pass through. How come it mentions this as a second directory? (3) i commented the above [ defaults] with a ; and I get another error: Fatal error:Syntax error - File ffoplsaanb.itp, line 1Last line read:'[ atomtypes ]'Invalid order for directive atomtypes which might mean according to what I have read (correct me if I am wrong please), that the order might be violated and that [atomtypes] should not come first; but it is the first directive in the ffoplsaanb.itp file, which should be read first. So what might be happening? what is going wrong? or maybe what am I missing?Thank you all once again for the effort you are making in this forum It seems like the format of whatever files you're using is horribly broken. I would recommend starting over and not making any adjustments to any files (removing lines, changing contents, adding comments, etc) unless you know exactly what you're doing. For example, the presence of '\par' in ffoplsaamod.itp suggests wrong line endings (i.e. from not using a plain text editor). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] equilibrium for box of simulation
On 5/10/2012 12:06 AM, mohammad agha wrote: Dear GROMACS Users, I asked this question before but I don't understand it! I placed several materials in my box of simulation for example box with 6nm*6nm*6nm and my materials are not placed in the smaller box but when I equilibrate my system, the box became smaller and temperature and pressure also equilibrate. my question is: is my system and equilibrate mistake, because of reach to smaller box? Is there equilibriums with reach to smaller box? At least one of your volume, contents or model physics are not consistent with the others, but only you can say which. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction study for peptide-receptor..
On 10/4/12 9:16 AM, rama david wrote: Thank you for reply, I read the recently published article in Biochemistry. They worked on the same receptor that I am working. ( as I mention in my previous mail) They used NAMD software and I am using gromacs. They sliced the receptor binding site and used the the solid support to the binding site and did simulation. So if I freeze the group is it will ok ?? I've already stated my opinion on this matter, so I won't state it again. I will not try to pre-judge a study I have not read (regarding the solid support) but it seems to me that if you are analyzing the binding of a peptide to a protein, that is fairly straightforward MD without anything fancy. Is it possible in gromacs to fix the residue on solid immobilized surface. If it is how to do it?? Build a surface, create a merged moleculetype, and define bonds between protein atoms and surface atoms. This all sounds like a ridiculous amount of work. my question is How to decide which group are remove and which group should keep in simulation. IMHO, it's not worth doing in this way. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] equilibrium for box of simulation
On 10/4/12 10:06 AM, mohammad agha wrote: Dear GROMACS Users, I asked this question before but I don't understand it! I placed several materials in my box of simulation for example box with 6nm*6nm*6nm and my materials are not placed in the smaller box but when I equilibrate my system, the box became smaller and temperature and pressure also equilibrate. my question is: is my system and equilibrate mistake, because of reach to smaller box? Is there equilibriums with reach to smaller box? What do you mean by my materials are not placed in the smaller box? If a box compresses, it is because the initial configuration was incompatible with the desired equilibration conditions and it contracted produce the desired quantity (likely pressure). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/4/12 10:12 AM, Elie M wrote: Hello everyone, Justin, I have repeated the procedures without doing any changes and it does seem that you were right about the broken file. However now I get a different set of errors: (1) ERROR 1 [file ffoplsaabon.itp, line 2692]: Incorrect number of atomtypes for dihedral (4 instead of 2 or 4) (2) ERROR 2 [file ffoplsaabon.itp, line 2694]: Not enough parameters You should inspect ffoplsaabon.itp to see what is on these lines. It is odd that grompp would complain about standard force field files if they have not been changed. and then a lot of errors of the type: ERROR 3 [file S54.top, line 118]: No default Bond types ERROR 4 [file S54.top, line 120]: No default Bond types ERROR 5 [file S54.top, line 124]: No default Bond types ERROR 6 [file S54.top, line 127]: No default Bond types... Maybe the main question is for the third error is how to define these bond types and angles? If a certain interaction is not available in ffbonded.itp (i.e. you've got bonds that are not parameterized in the chosen force field) you need to add them either in ffbonded.itp (potentially dangerous, given the previous posts) or directly in the topology (probably safer). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] equilibrium for box of simulation
Dear Justin, my materials are not placed in the smaller box means if I select box with dimensions 5.99 nm, space is low and insufficient for my molecules! but after equilibrate the box become small. According what you said, when the box become smaller in equilibrium, there is not mistake and it is natural? Best Regards Sara - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, October 4, 2012 5:52 PM Subject: Re: [gmx-users] equilibrium for box of simulation On 10/4/12 10:06 AM, mohammad agha wrote: Dear GROMACS Users, I asked this question before but I don't understand it! I placed several materials in my box of simulation for example box with 6nm*6nm*6nm and my materials are not placed in the smaller box but when I equilibrate my system, the box became smaller and temperature and pressure also equilibrate. my question is: is my system and equilibrate mistake, because of reach to smaller box? Is there equilibriums with reach to smaller box? What do you mean by my materials are not placed in the smaller box? If a box compresses, it is because the initial configuration was incompatible with the desired equilibration conditions and it contracted produce the desired quantity (likely pressure). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] equilibrium for box of simulation
Dear Mark, So, when in the equilibrium stage, the box become small, there is one mistake in my system? I don't know where is my mistake! Best Regards Sara - Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, October 4, 2012 5:48 PM Subject: Re: [gmx-users] equilibrium for box of simulation On 5/10/2012 12:06 AM, mohammad agha wrote: Dear GROMACS Users, I asked this question before but I don't understand it! I placed several materials in my box of simulation for example box with 6nm*6nm*6nm and my materials are not placed in the smaller box but when I equilibrate my system, the box became smaller and temperature and pressure also equilibrate. my question is: is my system and equilibrate mistake, because of reach to smaller box? Is there equilibriums with reach to smaller box? At least one of your volume, contents or model physics are not consistent with the others, but only you can say which. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] equilibrium for box of simulation
On 10/4/12 10:38 AM, mohammad agha wrote: Dear Justin, my materials are not placed in the smaller box means if I select box with dimensions 5.99 nm, space is low and insufficient for my molecules! but after equilibrate the box become small. Please define what you mean here. You start with a 6-nm cubic box. How small does it get? Are the box vectors trending downward, or do they converge? What is the change in density, and is it acceptable? According what you said, when the box become smaller in equilibrium, there is not mistake and it is natural? That depends on the magnitude of the change. Compression indicates that the pressure (and thus density of the system) was not at the desired value and the system is contracting. The manner in which the contraction occurs (magnitude, speed) is the deciding factor as to whether or not there is a problem. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: Re: Binding Energy to Binding affinity (Kd) (Justin Lemkul)
Justin Lemkul wrote On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote: Hi Justin, I used ~20 windows to sample ~2 nm pulling. I notice that the distance between the complex being increased during the pulling but not gradually. At the distance of 0-1nm, there are 70 snapshots (the distance sometime increased sometimes decreased). At the distance of 1-2nm, there are only 30 snapshots (the distance kept increasing always). At the distance more than 3nm, the distance increased as 0.3nm of each snapshot, is it normal and reliable? I will assume you are using a harmonic potential (umbrella) to do the pulling. In this case, your observations are totally normal. When two species interact strongly, it is harder to pull them apart, thus the spring extends further to induce a larger force before displacement occurs. As the restoring forces are overcome, it is easier to move the pulled group through solution, so it makes more steady progress as the molecules are separated. Hi Justin, it is right I am using umbrella pulling. Now here is another hurdle in front of me: How to select the snapshots for umbrella samples? Since the distance between two groups went higher or lower at the beginning of the pulling. For example, during the pulling simulation, the distance changes like: 0.46 0.42 0.46 0.43 0.44 0.42 0.45 0.44 0.43 0.45 0.44 0.45 0.43 0.44 0.44 0.54 0.52 0.63 0.65 0.72 0.8 0.92 1.2 1.5 (nm) . I suppose it doesn't matter which snapshots to be chosen, as long as the snapshots can indicate a good spacing, the PMF result always should be same, right? Thanks, jiang. -- View this message in context: http://gromacs.5086.n6.nabble.com/RE-Re-Binding-Energy-to-Binding-affinity-Kd-Justin-Lemkul-tp5001504p5001632.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RE: Re: Binding Energy to Binding affinity (Kd) (Justin Lemkul)
On 10/4/12 10:52 AM, jiang wrote: Justin Lemkul wrote On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote: Hi Justin, I used ~20 windows to sample ~2 nm pulling. I notice that the distance between the complex being increased during the pulling but not gradually. At the distance of 0-1nm, there are 70 snapshots (the distance sometime increased sometimes decreased). At the distance of 1-2nm, there are only 30 snapshots (the distance kept increasing always). At the distance more than 3nm, the distance increased as 0.3nm of each snapshot, is it normal and reliable? I will assume you are using a harmonic potential (umbrella) to do the pulling. In this case, your observations are totally normal. When two species interact strongly, it is harder to pull them apart, thus the spring extends further to induce a larger force before displacement occurs. As the restoring forces are overcome, it is easier to move the pulled group through solution, so it makes more steady progress as the molecules are separated. Hi Justin, it is right I am using umbrella pulling. Now here is another hurdle in front of me: How to select the snapshots for umbrella samples? Since the distance between two groups went higher or lower at the beginning of the pulling. For example, during the pulling simulation, the distance changes like: 0.46 0.42 0.46 0.43 0.44 0.42 0.45 0.44 0.43 0.45 0.44 0.45 0.43 0.44 0.44 0.54 0.52 0.63 0.65 0.72 0.8 0.92 1.2 1.5 (nm) . I suppose it doesn't matter which snapshots to be chosen, as long as the snapshots can indicate a good spacing, the PMF result always should be same, right? You need reasonable spacing and sufficient sampling in each window to allow for proper overlap of the umbrella potentials. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: Re: Binding Energy to Binding affinity (Kd)
You could use 'constraint' pull-mode instead of the 'umbrella' mode. Than the distance would change gradually and you won't observe the fluctuations in the distance. greetings thomas Am 04.10.2012 16:58, schrieb gmx-users-requ...@gromacs.org: On 10/4/12 10:52 AM, jiang wrote: Justin Lemkul wrote On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote: Hi Justin, I used ~20 windows to sample ~2 nm pulling. I notice that the distance between the complex being increased during the pulling but not gradually. At the distance of 0-1nm, there are 70 snapshots (the distance sometime increased sometimes decreased). At the distance of 1-2nm, there are only 30 snapshots (the distance kept increasing always). At the distance more than 3nm, the distance increased as 0.3nm of each snapshot, is it normal and reliable? I will assume you are using a harmonic potential (umbrella) to do the pulling. In this case, your observations are totally normal. When two species interact strongly, it is harder to pull them apart, thus the spring extends further to induce a larger force before displacement occurs. As the restoring forces are overcome, it is easier to move the pulled group through solution, so it makes more steady progress as the molecules are separated. Hi Justin, it is right I am using umbrella pulling. Now here is another hurdle in front of me: How to select the snapshots for umbrella samples? Since the distance between two groups went higher or lower at the beginning of the pulling. For example, during the pulling simulation, the distance changes like: 0.46 0.42 0.46 0.43 0.44 0.42 0.45 0.44 0.43 0.45 0.44 0.45 0.43 0.44 0.44 0.54 0.52 0.63 0.65 0.72 0.8 0.92 1.2 1.5 (nm) . I suppose it doesn't matter which snapshots to be chosen, as long as the snapshots can indicate a good spacing, the PMF result always should be same, right? You need reasonable spacing and sufficient sampling in each window to allow for proper overlap of the umbrella potentials. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: equilibrium for box of simulation
Please keep the discussion on the gmx-users list. On 10/4/12 11:28 AM, mohammad agha wrote: Dear Justin, Thank you very much from your help. I don't know about vectors trending downward, or do they converge You can plot box vectors from the .edr file. That will give you their values and show trends in the data. The change of density is from 1274 to 1685. and the slope of increasing the density at the first is much and then it become almost fix. This outcome suggests that your box likely has stabilized. You should still plot the vectors to understand what's going on. You also need to assess whether or not this density is acceptable as an evaluation of your physical model of the system. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: vmd-l: Re: compiling VMD with gcc 4.7
Dear All, I spent two days converting a .top file from gromos53a6 to one readable by VMD/NAMD. Now I am about to begin the ffbonded/nonbonded to a readable format for the same and would like to know beforehand if anyone has already done this so I can just use the library? Most are straightforward conversions of format. The main prblem is the NAMD (I believe) does not already have the parameters for cg or merged CH croups. The gromos force fields for gromacs only do this with chain non-polar, leaving the charged H groups alone. I did find however, no equivalent with trying to first generate a .psf file, and then looking at the vdw /angle, dihedrals and non bonded files for NAMD. Example a methyl is CH3 with a mass of 15.00 CH2 Mass 14 ,etc with only 3 atom type changes, you would think it wouldnt be so painfull, but it turns into a hellish nightmare. Any links or pointers would be appreciated, however I already assume I have to do this myself to use the VMD tools with Gromacs traj. Its still shorter than 3 months of simulations with a new index file. Sincerely, Stephan Watkins -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding g_covar
Hello Everybody, I am using g_covar with -xpmc flag in-oder to generate matrix of atomic correlation coefficients. At present I am using g_covar script given by Ran, which I downloaded from gromacs user modified script pool. Since Ran's script is for gromacs 3.3.3 and it not accept .trp input from upgraded version (eg 4.5.5). Anybody have upgraded g_covar which can do the same job. regards Vidya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp; I have commented ; one line which was given the first two errors. Now the only errors remaining are the bonds, angles and some others. How to correct these? For example one of them is (the error occuring at line 118 which is no different from others). 111 [ bonds ] 112 ; aiaj functc0c1 c2c3 113 1 2 1 114 1 5 1 115 1 47 1 116 2 3 1 117 248 1 118 3 4 1 How can the source of error be known and corrected? Elie Date: Thu, 4 Oct 2012 10:26:04 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/4/12 10:12 AM, Elie M wrote: Hello everyone, Justin, I have repeated the procedures without doing any changes and it does seem that you were right about the broken file. However now I get a different set of errors: (1) ERROR 1 [file ffoplsaabon.itp, line 2692]: Incorrect number of atomtypes for dihedral (4 instead of 2 or 4) (2) ERROR 2 [file ffoplsaabon.itp, line 2694]: Not enough parameters You should inspect ffoplsaabon.itp to see what is on these lines. It is odd that grompp would complain about standard force field files if they have not been changed. and then a lot of errors of the type: ERROR 3 [file S54.top, line 118]: No default Bond types ERROR 4 [file S54.top, line 120]: No default Bond types ERROR 5 [file S54.top, line 124]: No default Bond types ERROR 6 [file S54.top, line 127]: No default Bond types... Maybe the main question is for the third error is how to define these bond types and angles? If a certain interaction is not available in ffbonded.itp (i.e. you've got bonds that are not parameterized in the chosen force field) you need to add them either in ffbonded.itp (potentially dangerous, given the previous posts) or directly in the topology (probably safer). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] equilibrium for box of simulation
Dear Justin, Thank you very much from your help. Oh, yes, the vectors of box are downward in the first with much slope and then the slope became milder and milder and then it become almost fix. For checking of density, should I use from formula: d=m/v? Best Regards Sara - Original Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, October 4, 2012 7:01 PM Subject: Re: equilibrium for box of simulation Please keep the discussion on the gmx-users list. On 10/4/12 11:28 AM, mohammad agha wrote: Dear Justin, Thank you very much from your help. I don't know about vectors trending downward, or do they converge You can plot box vectors from the .edr file. That will give you their values and show trends in the data. The change of density is from 1274 to 1685. and the slope of increasing the density at the first is much and then it become almost fix. This outcome suggests that your box likely has stabilized. You should still plot the vectors to understand what's going on. You also need to assess whether or not this density is acceptable as an evaluation of your physical model of the system. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/4/12 12:13 PM, Elie M wrote: Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp; I have commented ; one line which was given the first two errors. Now the only errors remaining are the bonds, angles and some others. How to correct these? For example one of them is (the error occuring at line 118 which is no different from others). 111 [ bonds ] 112 ; aiaj functc0c1 c2c3 113 1 2 1 114 1 5 1 115 147 1 116 2 3 1 117 248 1 118 3 4 1 How can the source of error be known and corrected? The error message means that no suitable parameters exist in the force field for the bond that occurs between those atoms. You either need to parameterize the problematic bond(s) yourself or obtain parameters from some other reliable source. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] equilibrium for box of simulation
On 10/4/12 12:25 PM, mohammad agha wrote: Dear Justin, Thank you very much from your help. Oh, yes, the vectors of box are downward in the first with much slope and then the slope became milder and milder and then it become almost fix. For checking of density, should I use from formula: d=m/v? You already have the density value; you posted it before. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About Lipid Protein simualtion
Dear Justin , Thank you for you Previous reply. I am doing Simulation of Cyclic Peptide in Lipids I am following your tutorial When I use inflategro script For my System I have got Output System_inflated.gro file with certain message in Command prompt as follows . The Below Message Shows That There is No Lipid Molecules Are Deleted Should I Change the Cut-off or scaling Factor to Delete the Lipid Molecules or is it enough , I Mean Must Some Lipid Molecules Need to be Deleted ? There are 128 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower leaflet Centering protein Checking for overlap ...this might actually take a while 100 % done... There are 0 lipids within cut-off range... 0 will be removed from the upper leaflet... 0 will be removed from the lower leaflet... Writing scaled bilayer centered protein... Calculating Area per lipid... Protein X-min/max: 19 40 Protein Y-min/max: 21 39 X-range: 21 A Y-range: 18 A Building 21 X 18 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 4 nm^2 Area per lipid: 8.9375 nm^2 Area per protein, upper half: 3.5 nm^2 Area per lipid, upper leaflet : 8.9453125 nm^2 Area per protein, lower half: 3.5 nm^2 Area per lipid, lower leaflet : 8.9453125 nm^2 Writing Area per lipid... Done! 2) Also When I Run Grompp for EM Which Topology Should I use ? I have used my Multi chain protein.top When I Have used that I got Error AS follows Fatal error: [ file strong_porse.itp, line 8 ]: Atom index (4) in position_restraints out of bounds (1-3). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS How to Rectify the Problem? Thanks In Advance With High Regards S.Vidhyasankar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About Lipid Protein simualtion
On 10/4/12 1:12 PM, vidhya sankar wrote: Dear Justin , Thank you for you Previous reply. I am doing Simulation of Cyclic Peptide in Lipids I am following your tutorial When I use inflategro script For my System I have got Output System_inflated.gro file with certain message in Command prompt as follows . The Below Message Shows That There is No Lipid Molecules Are Deleted Should I Change the Cut-off or scaling Factor to Delete the Lipid Molecules or is it enough , I Mean Must Some Lipid Molecules Need to be Deleted ? It would be highly unusual if no lipids were deleted, unless the protein is not actually embedded in the membrane. There are 128 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower leaflet Centering protein Checking for overlap ...this might actually take a while 100 % done... There are 0 lipids within cut-off range... 0 will be removed from the upper leaflet... 0 will be removed from the lower leaflet... Writing scaled bilayer centered protein... Calculating Area per lipid... Protein X-min/max: 1940 Protein Y-min/max: 2139 X-range: 21 AY-range: 18 A Building 21 X 18 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 4 nm^2 Area per lipid: 8.9375 nm^2 Area per protein, upper half: 3.5 nm^2 Area per lipid, upper leaflet : 8.9453125 nm^2 Area per protein, lower half: 3.5 nm^2 Area per lipid, lower leaflet : 8.9453125 nm^2 Writing Area per lipid... Done! 2) Also When I Run Grompp for EM Which Topology Should I use ? I have used my Multi chain protein.top When I Have used that I got Error AS follows Fatal error: [ file strong_porse.itp, line 8 ]: Atom index (4) in position_restraints out of bounds (1-3). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS How to Rectify the Problem? Position restraints can only be applied within a given [moleculetype]. Note that the error is explained on the Gromacs website, along with an example of proper usage: http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
I guess now I get what is happening finally. Correct me if I am wrong. The .top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which was also modified to include atoms that were not there *but present in atomtypes.atp). The .top file describes all the bonds and angles in the molecule. This was successful. However the characteristics of some of those bonds are not described in the foplssabon.itp file; for example I have Sulfur in my molecule connected to carbon which has no entry in foplsaabon.itp and must be added to that file manually. I guess now I am in a position to check those bonds and add the relevant information which i will gather maybe from HYPERCHEM or ARGUSLAB??A final question is in order here: what do the parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and in what units? Thank you very much Elie Date: Thu, 4 Oct 2012 12:25:48 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/4/12 12:13 PM, Elie M wrote: Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp; I have commented ; one line which was given the first two errors. Now the only errors remaining are the bonds, angles and some others. How to correct these? For example one of them is (the error occuring at line 118 which is no different from others). 111 [ bonds ] 112 ; aiaj functc0c1 c2c3 113 1 2 1 114 1 5 1 115 147 1 116 2 3 1 117 248 1 118 3 4 1 How can the source of error be known and corrected? The error message means that no suitable parameters exist in the force field for the bond that occurs between those atoms. You either need to parameterize the problematic bond(s) yourself or obtain parameters from some other reliable source. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/4/12 4:22 PM, Elie M wrote: I guess now I get what is happening finally. Correct me if I am wrong. The .top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which was also modified to include atoms that were not there *but present in atomtypes.atp). The .top file describes all the bonds and angles in the molecule. This was successful. However the characteristics of some of those bonds are not described in the foplssabon.itp file; for example I have Sulfur in my molecule connected to carbon which has no entry in foplsaabon.itp and must be added to that file manually. I guess now I am in a position to check those bonds and add the relevant information which i will gather maybe from HYPERCHEM or ARGUSLAB??A final question is in order here: what do the You will have to calculate reasonable values in some way, yes. parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and in what units? All of this is in the manual. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error There is no domain decomposition for 6 nodes that is compatible
Hi, I am performing a free energy calculation based on Justin Lemkul's tutorial. My system is a protein in water and dodecane and I'm coupling the protein considering none to only vdw interactions for my lambda 0 and 1 states. However, I get this error when trying to minimize the system: Fatal error: There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum cell size of 7.55833 nm min1.0.mdp http://gromacs.5086.n6.nabble.com/file/n5001648/min1.0.mdp Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition I know I can fix easily this problem by using -nt 1 option. But I still want to use all available cores. I suspect the error is in the mdp file because if I use the following mdp file for the minimization it works. title = cpeptide cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Obviously this mdp file does not work for free energy calculations. I still want to use the attached one, but I don´t know what to change to make it work. This is the link for my log and mdp file. mdp_and_log_files.zip http://gromacs.5086.n6.nabble.com/file/n5001648/mdp_and_log_files.zip Thank you in advance, Sonia Aguilera Graduate Assistant Universidad de los Andes-Colombia -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-There-is-no-domain-decomposition-for-6-nodes-that-is-compatible-tp5001648.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error There is no domain decomposition for 6 nodes that is compatible
On 10/4/12 4:54 PM, Sonia Aguilera wrote: Hi, I am performing a free energy calculation based on Justin Lemkul's tutorial. My system is a protein in water and dodecane and I'm coupling the protein considering none to only vdw interactions for my lambda 0 and 1 states. However, I get this error when trying to minimize the system: Fatal error: There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum cell size of 7.55833 nm min1.0.mdp http://gromacs.5086.n6.nabble.com/file/n5001648/min1.0.mdp Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition I know I can fix easily this problem by using -nt 1 option. But I still want to use all available cores. I suspect the error is in the mdp file because if I use the following mdp file for the minimization it works. title = cpeptide cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Obviously this mdp file does not work for free energy calculations. I still want to use the attached one, but I don´t know what to change to make it work. This is the link for my log and mdp file. mdp_and_log_files.zip http://gromacs.5086.n6.nabble.com/file/n5001648/mdp_and_log_files.zip The problem comes from these settings: couple-moltype = Protein_chain_A ; name of moleculetype to decouple couple-lambda0 = none ; turn off everything couple-lambda1 = vdw ; only van der Waals interactions couple-intramol = no You're transforming the protein using long-range exclusions and pair interactions (couple-intramol = no). These interactions make the required DD cell size very large. Then you run into the fact that you can't decompose any system into any arbitrary number of DD cells, because their size is limited by the bonded interactions, pairs, cutoffs, and other factors. http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: vmd-l: Re: compiling VMD with gcc 4.7
On 5/10/2012 1:49 AM, lloyd riggs wrote: Please choose descriptive subjects and start new email messages when posting to mailing lists. This makes people better able to respond to you by allowing mail reading software to work properly. Cross-posting to the VMD and GROMACS lists when your question relates to conversion of file formats between GROMACS and NAMD seems a bit strange, too. Dear All, I spent two days converting a .top file from gromos53a6 to one readable by VMD/NAMD. Now I am about to begin the ffbonded/nonbonded to a readable format for the same and would like to know beforehand if anyone has already done this so I can just use the library? Most are straightforward conversions of format. The main prblem is the NAMD (I believe) does not already have the parameters for cg or merged CH croups. The gromos force fields for gromacs only do this with chain non-polar, leaving the charged H groups alone. I did find however, no equivalent with trying to first generate a .psf file, and then looking at the vdw /angle, dihedrals and non bonded files for NAMD. Example a methyl is CH3 with a mass of 15.00 CH2 Mass 14 ,etc with only 3 atom type changes, you would think it wouldnt be so painfull, but it turns into a hellish nightmare. I don't understand what the problem is from this description. Any links or pointers would be appreciated, however I already assume I have to do this myself to use the VMD tools with Gromacs traj. Its still shorter than 3 months of simulations with a new index file. VMD can just read a gromacs trajectory. What's the problem with that? Why do you (think you) need a matching .psf? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with the installation of Gromacs 4-5.5
On 4/10/2012 3:37 PM, Deepak Ojha wrote: Dear All I want to use Amber force field in Gromacs therefore I installed the latest version of Gromacs and installed accordingly as per as the instructions given in INSTALL.automake file. ./configure make make install It works fine and shows the message that installation is complete but none of the commands like pdb2gmx,mdrun works.Even the luck does not works which is meant to test the installation of gromacs. What is the issue with the installation.Please help me resolve it. http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] The No. of the CO2 melecules in top file can not be updated correctly.
Hi, all, I am still working on the molecular simulation of CO2 and H2O mixture. The information of the molecules types and the force field model are all defined in the a.top file. 1 [ defaults ] 2 ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 3 1 3 yes 0.50.5 4 [ atomtypes ] 5 ; type at.nummasschargeptypesigmaepsilon 6 CO 6 12.01100.5888A 0.27918 0.2398 7 OC 8 15.9994 -0.2944A 0.3 0.6872 8 OW 6 15.99940 -0.8476A 0.316557 0.650194 9 HW 1 1.008000.4238A 0.0 0.0 10 [ moleculetype ] 11 ;name nrexcl 12 CO2 3 13 [atoms] 14 ; nr type resnr residue atom cgnr charge mass 32 [moleculetype] 33 ; molname nrexcl 34 SOL 2 35 [atoms] 36 ; nr type resnr residue atom cgnr charge mass ... 47 [system] 48 sparkling water 49 [molecules] 50 CO2 100 51 SOL 3000 I create on co2.gro file to put one CO2 molecule inside. Then I used genbox -ci co2.gro -nmol 190 -o a.gro -box 7. -p a.top to put 190 CO2 molecules inside the box. Then I used genbox -cp a.gro -o b.gro -box 7 -cs -maxsol 9810 -p a.top to put 9810 H2O molecules inside the box. In the file a.top, the No. of the H2O was updated correctly, while the No. of the CO2 molecules was not updated. The No. of the atoms in .gro files are correct. Can you please tell me the reason or how to solve it? Thank you very much. Best Retards, Kai -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The No. of the CO2 melecules in top file can not be updated correctly.
On 10/4/12 5:29 PM, Bao Kai wrote: Hi, all, I am still working on the molecular simulation of CO2 and H2O mixture. The information of the molecules types and the force field model are all defined in the a.top file. 1 [ defaults ] 2 ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 3 1 3 yes 0.50.5 4 [ atomtypes ] 5 ; type at.nummasschargeptypesigmaepsilon 6 CO 6 12.01100.5888A 0.27918 0.2398 7 OC 8 15.9994 -0.2944A 0.3 0.6872 8 OW 6 15.99940 -0.8476A 0.316557 0.650194 9 HW 1 1.008000.4238A 0.0 0.0 10 [ moleculetype ] 11 ;name nrexcl 12 CO2 3 13 [atoms] 14 ; nr type resnr residue atom cgnr charge mass 32 [moleculetype] 33 ; molname nrexcl 34 SOL 2 35 [atoms] 36 ; nr type resnr residue atom cgnr charge mass ... 47 [system] 48 sparkling water 49 [molecules] 50 CO2 100 51 SOL 3000 I create on co2.gro file to put one CO2 molecule inside. Then I used genbox -ci co2.gro -nmol 190 -o a.gro -box 7. -p a.top to put 190 CO2 molecules inside the box. Then I used genbox -cp a.gro -o b.gro -box 7 -cs -maxsol 9810 -p a.top to put 9810 H2O molecules inside the box. In the file a.top, the No. of the H2O was updated correctly, while the No. of the CO2 molecules was not updated. The No. of the atoms in .gro files are correct. Can you please tell me the reason or how to solve it? genbox only updates water molecules in the topology. Anything else is up to you. Beware that a linear, 3-atom model of CO2 is probably not going to work due to issues with linear angles, as has been discussed frequently on the list. A more robust approach involves virtual sites. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Error with grompp
I guess the first parameter of each pair is easy to find. what about kb? k theta?. kb is the force constant isnt it? any reference about a method how to calculate them please? pr anything atht might be of help. Elie Date: Thu, 4 Oct 2012 16:25:35 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Error with grompp On 10/4/12 4:22 PM, Elie M wrote: I guess now I get what is happening finally. Correct me if I am wrong. The .top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which was also modified to include atoms that were not there *but present in atomtypes.atp). The .top file describes all the bonds and angles in the molecule. This was successful. However the characteristics of some of those bonds are not described in the foplssabon.itp file; for example I have Sulfur in my molecule connected to carbon which has no entry in foplsaabon.itp and must be added to that file manually. I guess now I am in a position to check those bonds and add the relevant information which i will gather maybe from HYPERCHEM or ARGUSLAB??A final question is in order here: what do the You will have to calculate reasonable values in some way, yes. parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and in what units? All of this is in the manual. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with grompp
On 10/4/12 5:56 PM, Elie M wrote: I guess the first parameter of each pair is easy to find. what about kb? k theta?. kb is the force constant isnt it? any reference about a method how to calculate them please? pr anything atht might be of help. Bonded parameters are generally based on vibrational spectra and X-ray data. For OPLS, the bonded parameters were originally taken from an AMBER parameter set in the mid-1980's and have some terms have subsequently been revised over time. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] equilibrium for box of simulation
Dear Justin, Thank you very much. So, decreasing of box dimensions is not bad, if all thing process natural, yes? The cause of my doubt was because of in the most of articles was said for example we select box with dimensions 10nm that after equilibrium was converted to 11nm and I didn't see the report of decreasing of box dimensions! May I know your idea about it, Please? Best Regards Sara - Original Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, October 4, 2012 7:57 PM Subject: Re: [gmx-users] equilibrium for box of simulation On 10/4/12 12:25 PM, mohammad agha wrote: Dear Justin, Thank you very much from your help. Oh, yes, the vectors of box are downward in the first with much slope and then the slope became milder and milder and then it become almost fix. For checking of density, should I use from formula: d=m/v? You already have the density value; you posted it before. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists