[gmx-users] Re: gmx-users Digest, Vol 60, Issue 40
Dear All, Please see my questions inline below. Thanks again for your help. Darrell >darre...@ece.ubc.ca wrote: >> Dear All, >> I am resubmitting my question below as I did not receive a response and >> am thinking that my previous e-mail was not recognized by the system or >> missed. Could someone please provide me with an answer to my questions >> below? >> >> Many thanks. >> >> Darrell Koskinen >> >> On 4/2/2009, "" <> wrote: >> Date: Wed, 01 Apr 2009 22:38:28 +0200 From: David van der Spoel Subject: Re: [gmx-users] x2top & Encad all-atom force field (vacuum) not recognizing bonds To: Discussion list for GROMACS users Message-ID: <49d3d0c4.4040...@xray.bmc.uu.se> Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: > Dear All, > I have been trying to determine why I am experiencing problems when I run > a gromacs file through x2top. I have checked my gromacs file with VMD to > ensure that the file is correct and VMD validates that my file is > correct as I see the intended structure. Thus, the atoms are indeed > located within reasonable distance from each other such that x2top > should be recognizing the bonds. > > Here is an extract from my gromacs file: > > 2Grph C1 0.000 0.000 0.000 0. 0. 0. > 2Grph C2 0.071 -0.123 0.000 0. 0. 0. > 2Grph C3 0.071 0.123 0.000 0. 0. 0. > 2Grph C4 -0.142 0.000 0.000 0. 0. 0. > 2Grph C5 -0.000 -0.250 0.000 0. 0. 0. > 2Grph C6 0.210 -0.120 0.000 0. 0. 0. > > I thought that in order to make x2top work correctly that I would have to > modify the files as described in Christopher Stiles website > (http://cs86.com/CNSE/SWNT.htm). I made the specified changes to the > following files and saved them in my working directory: > ffencadv.n2t > ffgmx.n2t > ffgmxbon.itp > > I also changed the name of ffgmxbon.itp to ffencadvbon.itp as I read in > one post that this file should be renamed as such. > > After all these changes, I still experience a problem when I run the > command: > x2top -ff select -f graphene_nm.gro -o graphene_nm.top > selecting option 7: Encad all-atom force field, using scaled-down vacuum > charges > > When I run the above command, I receive output telling me that the atoms > have 0 bonds. An extract of the output appears below for your reference. > Can not find forcefield for atom H-266 with 0 bonds > Can not find forcefield for atom H-267 with 0 bonds > Can not find forcefield for atom H-268 with 0 bonds > Can not find forcefield for atom H-269 with 0 bonds > Can not find forcefield for atom H-270 with 0 bonds Could there still be an error in your gro file, as it seems to contain only C, and the error message points to H. x2top might work slightly better in 4.0.x. And by the way, this tutorial may be slightly confusing. The only thing you need to do is edit the .n2t file corresponding to your force field. I don't recall what is supplied in 3.3, but in 4.0 it is ffoplsaa.n2t. >>> My gro file does contain H atoms as well. In my extract of the gro file I >>> only showed the first few lines of the gro file and these lines only >>> have C atoms. Note that I receive the same message for the C atoms (i.e. >>> "Can not find forcefield for atom C-1 with 0 bonds"). >>> >>> I actually created the files ffencadv.n2t & ffgmx.n2t in my working >>> directory since the only n2t file I could find in the gromacs directory >>> was the ffoplsaa.n2t file and the tutorial did not mention the >>> ffoplsaa.n2t file. Should I be modifying the ffoplsaa.n2t file instead? >>> If so, can you please provide me some direction on what needs to be >>> added to this file so that it recognizes the atoms in my graphene >>> structure as I looked at this file but do not understand what some of >>> the columns represent. >>> >>> Also, I thought that ffoplsaa was to be used for liquids and since my >>> simulation is in an air environment, I thought that I should be using >>> the encad force field in a vacuum and should therefore be modifying an >>> encad n2t file. Please correct me if I am wrong. >Encad is not made for vacuum. You have to verify your force field >anyway, for publication purposes. OPLS will work just fine though. > > >>> >>> Also, could you also please explain the purpose of the n2t file as I >>> looked in the gromacs manual and see no description of files with the >>> n2t extension and their purpose. >Check archive of the mailing list. This tool will be replaced in the >near future (5.0), therefore there is no documentation. As suggested, I searched the mailing list using the keyword "n2t". The search ret
[gmx-users] the reson for neutralizing the charge
Hi Justin and all Thak you very much my problem solve. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Pressure Coupling Problem
Hi I am having some pressure coupling issues. I have a fairly large protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I run NVE it conserves energy with appropriate parameter settings. If I run NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello Rahman), the system just continuously expands. My parameters are as follows. Any ideas? Best, Ilya ; ; File 'mdout.mdp' was generated ; By user: relly (508) ; On host: master.simprota.com ; At date: Fri Mar 6 20:17:33 2009 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.004 ;nsteps = 25 nsteps = 250 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm_mode= linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm_grps= system ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 10 nstenergy= 10 ; Output frequency and precision for xtc file nstxtcout= 250 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = protein ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = .9 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon-r= 80 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = .9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1.e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = V-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 298.0 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 10 compressibility = 4.5e-5 ref_p= 1.01325 ; Scaling of reference coordinates, No, All or COM refcoord_scaling = No ; Random seed for Andersen thermostat andersen_seed= 815131 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Pressure Coupling Problem
Hi Ilya, First thing that comes to mind is that it is strange to couple a coulombic switching function with PME. While this could possibly be done correctly, I doubt that it is in fact done in the way that you expect (i.e. correctly) in gromacs. In fact, I think that grompp/mdrun should probably throw an error here -- unless it is actually handled in the proper way, and a developer could help you here to figure out if you are indeed getting what you desire. coulombtype = PME rcoulomb-switch = .9 rcoulomb = 1.0 However, it is not clear to me that this should cause a system to "continuously expand". Still, you do not give very good information about what you mean by "continuously expand". Can you please provide some information on that? e.g. amount of time and total volume change. Chris -- original message -- Hi I am having some pressure coupling issues. I have a fairly large protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I run NVE it conserves energy with appropriate parameter settings. If I run NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello Rahman), the system just continuously expands. My parameters are as follows. Any ideas? Best, Ilya ; ; File 'mdout.mdp' was generated ; By user: relly (508) ; On host: master.simprota.com ; At date: Fri Mar 6 20:17:33 2009 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.004 ;nsteps = 25 nsteps = 250 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm_mode= linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm_grps= system ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 10 nstenergy= 10 ; Output frequency and precision for xtc file nstxtcout= 250 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = protein ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = .9 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon-r= 80 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = .9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1.e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = V-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 298.0 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 10 compressibility = 4.5e-5 ref_p= 1.01325 ; Scaling of reference coordinates, No, All or COM refcoord_scaling = No ; Random seed for Andersen thermostat andersen_seed= 815131 ---
[gmx-users] distance restraints in Gromacs 4.0.4
Dear users I have found a problem for the distance constraint in the version 4.0.4 of gromacs. I am trying to simulate a water droplet around an ion. To do that I use a distance restraint armonic potential (pag.66, manual version 4). During my simulation the shape of my sphere fluctuating too much and many molecules leave the sphere even if the restoring force is big (I use for restraint armonic potential a constant k=1e4 KJ mol^-1 nm^-2 ). The problem disappear if I run the exactly same simulation with gromacs 3.3.3.:the spherical shape is always conserve and no molecules leave the sphere. Furthermore, if I am trying to run droplet larger than 1.0 nm radius (e.g. 1.6 nm). These simulation at a certain point stop, giving me the following error ** glibc detected *** Dmdrun: munmap_chunk(): invalid pointer: 0x00a72bd0 *** The same simulation in the version 3.3.3 runs without any problem. Do you know what kind of problem could be? Has the version 4.0.4 some problems with distance restrains? Thank you in advance for any help or suggestion Ivan Gladich -- --- Ivan Gladich Dreyfus Postdoctoral Fellow Department of Chemistry Purdue University 560 Oval Drive, box 140 West Lafayette IN 47906 USA Room: 265C Tel:765-494-5225 e-mail: iglad...@purdue.edu web page: http://web.ics.purdue.edu/~igladich/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Membrane protein tutorial
Hello all, Due to the recent influx in questions related to membrane proteins (especially with common questions), I decided to put together a step-by-step tutorial for membrane protein systems. It's a work in progress, so I would genuinely appreciate feedback from anyone who has a few minutes to take a look. These procedures make sense in my head, so hopefully that comes through in the instructions :) I have posted a link on the wiki site to my tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I hope that people find this useful. I have attempted to walk the user through most practical concerns that arise regarding topology organization and a few analysis questions that show up on the list frequently (g_order, g_density, etc). If you have comments or questions, please do not hesitate to send me a private message. -Justin -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_sdf
What exactly your issue with using g_sdf? You need to supple a trajectory, index, and topology. Index contains the three reference atoms for the molecule, plus the atom you are calculating the sdf to. Selection of the correct grid size and binwidth is required to get something that looks as you want it. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] missing interactions for the LJ-decoupled molecule during free energy in parallel but not serial
Thanks Berk, this makes sense to me. You were correct that my starting structure is fully Q+LJ coupled and it is only in the structures where there is no Q and I then couple LJ to lambda that I get this problem (and the extension that you suspect). I can just increase rdd. I was actually using couple-intramol=no, which should "leave on the intramolecular charge and LJ interactions" from the online manual mdp options page. Chris. -- original message -- Hi, I think this behavior is "expectable". The simplest explanation would be that some particles at the ends of the molecule only have LJ and no charge, I guess this is not the case. The more probable explanation is that your molecule extends when the LJ are turned off, since there are no interactions to hold it together anymore. There are two possible solutions: 1. increase -rdd (is by default guessed from the initial structure, which is probably compact. Not using domain decomposition completely removed the problem. 2. use couple-intramol to leave on the intramolecular charge and LJ interactions, this requires an extra (de-)coupling in vacuum to complete the cycle. Depending on your system removing or leaving on intramolecular interactions might lead to more efficient sampling. Berk Date: Mon, 6 Apr 2009 18:21:25 -0400 From: chris.neale at utoronto.ca To: gmx-users at gromacs.org Subject: [gmx-users] missing interactions for the LJ-decoupled molecule during free energy in parallel but not serial Hello, I am doing free energy calculations with gromacs 4.0.4. For the system I am using, I have reliable runs without any crashes when running in serial. When I run in parallel, I get stochastic crashes, that always have the same form (see below). Note that the "missing interactions" always involve the decoupled molecule and do not occur when decoupling the coulombics, but when decoupling the LJ interactions. I have included error messages below and then the mdp options. I will do some more tests to see if I can get rid of the problem by turning off domain decomposition and whatever else I can think of, but it strikes me that this may be related to the table representation of intramolecular interactions for the decoupled molecule not playing nice with domain decomposition. Any ideas here would be greatly appreciated. Thank you, Chris. ### From the stderr output ... ... A list of missing interactions: LJC Pairs NB of182 missing 10 exclusions of 86858 missing 10 Molecule type 'DPN' the first 10 missing interactions, except for exclusions: LJC Pairs NB atoms1 22 global 122 LJC Pairs NB atoms1 23 global 123 LJC Pairs NB atoms2 22 global 222 LJC Pairs NB atoms2 23 global 223 LJC Pairs NB atoms3 22 global 322 LJC Pairs NB atoms3 23 global 323 LJC Pairs NB atoms4 22 global 422 LJC Pairs NB atoms4 23 global 423 LJC Pairs NB atoms5 22 global 522 LJC Pairs NB atoms5 23 global 523 --- Program mdrun_mpi, VERSION 4.0.4 Source code file: domdec_top.c, line: 341 Fatal error: 20 of the 104681 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck # And in the .log file: ... ... Making 1D domain decomposition grid 2 x 1 x 1, home cell index 0 0 0 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: System There are: 42663 Atoms There are: 13807 VSites Charge group distribution at step 0: 7249 7314 Grid: 15 x 13 x 9 cells Initial temperature: 304.101 K Started mdrun on node 0 Sat Apr 4 09:49:03 2009 Step Time Lambda 0 2600.00.94000 Long Range LJ corr.: 1.9559e-04 Long Range LJ corr.: Epot -1071.93, Pres: -80.1596, Vir:1071.93 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 3.06434e+037.05100e+021.12328e+037.39277e+026.98859e+03 LJ (SR)LJ (LR) Disper. corr. Coulomb (SR) Coul. recip. 1.00381e+05 -3.08323e+03 -1.07193e+03 -6.15814e+05 -1.04726e+05 COM Pull En. PotentialKinetic En. Total EnergyTemperature 8.31361e-02 -6.11694e+051.07966e+05 -5.03728e+053.04185e+02 Pressure (bar) dVpot/dlambda dEkin/dlambda dG/dl constr. Cons. rmsd () 1.99373e+02 -2.95741e+010.0e+000.0e+004.34062e-06 Cons.2 rmsd () 4.
[gmx-users] Re: Gromacs QM-MM Tutorial
Hi Dr.Groenhof,
Thanks for the reply. I started working on that and than realized don't
have MOPAC plugged up with GROMACS. It took a while to get it running,
your installation comments were really helpful. I am below giving the
exact route to get the things working (little different from your tutorial
because of change in compiler version), might be of help to others.
Best Regards,
Praveen
Machine pentium dual core with Linux 2.6.24-23-generic 32 bit (i686)
1. downloaded gromacs-4.0.4 & libmopac.a from site
http://wwwuser.gwdg.de/~ggroenh/qmmm.html
2. libmopac.a goes to /usr/local/lib
3. Created test.c with
#include
__const unsigned short int **__wrap___ctype_b (void) {
return __ctype_b_loc();
}
4. cc -c test.c to creat test.o
5. ar rcv libtest.a test.o; ranlib libtest.a
6. libtest.a also goes to /usr/local/lib (libtest has been created to
avoid __ctype_b errors because
of mismatch between gcc compiler versions of current & the one which
created libmopac.a
7. ON bash shell:
export LDFLAGS="-L/usr/local/lib -Wl,--wrap,__ctype_b"
export CPPFLAGS=-DUSE_MOPAC
export LIBS="-lmopac -ltest"
8. in gromacs directory:
./configure --with-qmmm-mopac
make -j4
make install
This completes the compilation w/o any error. I am still to run any qmmm,
so cann't yet :( comment on the accuracy of process.
--
> The trick worked only in gromacs 3.2. You therefore have to use a
> different restrait, such as distance restraints. Hope this helps.
>
> Concerning the cys-cys dimerization, that depends how you do it. I am
> sorry I can not give a more concise answer to that question. Simplest
> would be to pull the S atoms together at MM level and perform short QM
> simulations with restraints on selected frames of the simulatoins.
> Hope this also helps.
> Gerrit
>
>
> On 6 Apr 2009, at 13:04, Praveen Agrawal wrote:
>
>> Hi Dr.Groenh,
>> Thankyou for sharing the tutorials on QMMM capabilities of Gromacs,
>> I am
>> following the same to be able to study cys-cys dimerization for short
>> membrane peptide. While following the tutorial I am getting errors
>> and am
>> unable to find any other details to overcome it, kindly help:
>>
>> 1. ERROR 1 virtual site CD (Res DAT-1) has non-zero mass 12.011
>> The 'trick' to create avoid virtual-virtual constraint treats atom
>> 7 as
>> virtual which is 'real' atom and has non zero mass. To overcome it I
>> did->
>> 2. 32 as combination of 7 &1 and 33 as combination of 16 & 14 but that
>> leads to the error: Cannot have constraint (32-33) with virtual site
>> (32)
>>
>> I am using Gromacs 4.0.3 and also attaching the corresponding file for
>> reference. Also, would want to have your opinion on: Is attempting
>> QM/MM
>> for cys-cys dimerization for short membrane peptide (25 amino acids
>> long
>> each) too far fetch idea?
>>
>> Best Regards,
>> Praveen
>> ~
>> http://www.scfbio-iitd.res.in
>> ~
>
> --
> Gerrit Groenhof
> MPI biophysical chemistry
> Goettingen
> Germany
> http://wwwuser.gwdg.de/~ggroenh/
>
~
http://www.scfbio-iitd.res.in
~
___
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[gmx-users] Doubt regarding membrane protein in POPC bilayer
Respected Sir, Thanks for your mail. I will work on this. Thanking you, Pawan On 4/7/09, Mark Abraham wrote: > > Pawan Kumar wrote: > >> Hello Sir, >> >> Can you please tell me how to couple ions with SOL ? >> Is there any command in gromacs to do that ? >> > > You need to define a group with SOL and the ions in an index file. This is > uses as input to grompp so that it can make sense of the same group name > when used in the .mdp file. See > http://wiki.gromacs.org/index.php/Index_File > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] md.mdp query
At the beginning of your md.mdp file you will see the following: ; RUN CONTROL PARAMETERS integrator = steep With this command you ask GROMACS to energy minimize your system by steepest descent. If you want to run a md simulation you will have to change the intergrator to md. You can read this, and more, in details in the manual. Good luck Antonia Date: Tue, 7 Apr 2009 17:16:03 +0530 From: bissoyi.akala...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] md.mdp query hello gromacs, i want to know the changes to be done in md.mdp files for 10 ns. i am trying to run it but it's showing the following message. Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 1000 Step=0, Dmax= 1.0e-02 nm, Epot= -5.01412e+06 Fmax= 3.66197e+03, atom= 4032 Step=2, Dmax= 5.0e-03 nm, Epot= -5.01438e+06 Fmax= 2.17491e+04, atom= 4032 Step=3, Dmax= 6.0e-03 nm, Epot= -5.01456e+06 Fmax= 9.13099e+03, atom= 4032 Step=5, Dmax= 3.6e-03 nm, Epot= -5.01468e+06 Fmax= 9.44298e+03, atom= 4032 Step= 10, Dmax= 2.7e-04 nm, Epot= -5.01470e+06 Fmax= 8.04093e+03, atom= 4032 Step= 11, Dmax= 3.2e-04 nm, Epot= -5.01472e+06 Fmax= 6.36864e+03, atom= 4032 Step= 12, Dmax= 3.9e-04 nm, Epot= -5.01474e+06 Fmax= 4.35105e+03, atom= 4032 Step= 14, Dmax= 2.3e-04 nm, Epot= -5.01476e+06 Fmax= 3.13319e+03, atom= 4032 Step= 16, Dmax= 1.4e-04 nm, Epot= -5.01478e+06 Fmax= 2.39737e+03, atom= 4032 Step= 18, Dmax= 8.4e-05 nm, Epot= -5.01478e+06 Fmax= 1.98224e+03, atom= 4032 Step= 21, Dmax= 2.5e-05 nm, Epot= -5.01479e+06 Fmax= 1.88313e+03, atom= 4034 Step= 22, Dmax= 3.0e-05 nm, Epot= -5.01479e+06 Fmax= 1.68824e+03, atom= 4032 Step= 23, Dmax= 3.6e-05 nm, Epot= -5.01479e+06 Fmax= 1.50693e+03, atom= 4032 Step= 25, Dmax= 2.2e-05 nm, Epot= -5.01479e+06 Fmax= 1.39532e+03, atom= 4032 Step= 26, Dmax= 2.6e-05 nm, Epot= -5.01480e+06 Fmax= 1.30313e+03, atom= 4032 Step= 27, Dmax= 3.1e-05 nm, Epot= -5.01481e+06 Fmax= 1.12668e+03, atom= 4034 Step= 28, Dmax= 3.8e-05 nm, Epot= -5.01482e+06 Fmax= 9.41676e+02, atom= 4034 Step= 30, Dmax= 2.3e-05 nm, Epot= -5.01483e+06 Fmax= 8.67996e+02, atom= 4032 Step= 31, Dmax= 2.7e-05 nm, Epot= -5.01483e+06 Fmax= 6.80316e+02, atom= 4034 Step= 32, Dmax= 3.2e-05 nm, Epot= -5.01484e+06 Fmax= 5.66923e+02, atom= 4034 Step= 33, Dmax= 3.9e-05 nm, Epot= -5.01485e+06 Fmax= 3.30411e+02, atom= 1881 Step= 35, Dmax= 2.3e-05 nm, Epot= -5.01487e+06 Fmax= 3.12606e+02, atom= 1881 Step= 37, Dmax= 1.4e-05 nm, Epot= -5.01488e+06 Fmax= 3.86990e+02, atom= 92925 Step= 38, Dmax= 1.7e-05 nm, Epot= -5.01489e+06 Fmax= 3.70596e+02, atom= 286823 Step= 40, Dmax= 1.0e-05 nm, Epot= -5.01489e+06 Fmax= 4.65471e+02, atom= 142601 Step= 41, Dmax= 1.2e-05 nm, Epot= -5.01490e+06 Fmax= 4.51394e+02, atom= 155810 Step= 43, Dmax= 7.3e-06 nm, Epot= -5.01490e+06 Fmax= 6.46500e+02, atom= 167601 Step= 47, Dmax= 1.1e-06 nm, Epot= -5.01490e+06 Fmax= 4.30994e+03, atom= 214498 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up traj.trr to ./#traj.trr.12# Back Off! I just backed up md.pdb to ./#md.pdb.8# Steepest Descents converged to machine precision in 48 steps, but did not reach the requested Fmax < 10. Potential Energy = -5.0149030e+06 Maximum force = 6.4650037e+02 on atom 167601 Norm of force = 7.3590344e+04 Kindly help me in this regard.I am attaching md.mdp file in which i have made the changes. -- akalabya N.I.T.Rourkela _ Show them the way! Add maps and directions to your party invites. http://www.microsoft.com/windows/windowslive/products/events.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] md.mdp query
Am 07.04.2009 um 13:46 schrieb akalabya bissoyi: hello gromacs, i want to know the changes to be done in md.mdp files for 10 ns. i am trying to run it but it's showing the following message. ... the following message is the output of an energy minimization and not a MD run. I suggest to do some reading and/or tutorials to get in touch with MD procedures in general. Parameters in mdp file are also described in the gromacs manual. Best wishes Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] md.mdp query
hello gromacs, i want to know the changes to be done in md.mdp files for 10 ns. i am trying to run it but it's showing the following message. Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 1000 Step=0, Dmax= 1.0e-02 nm, Epot= -5.01412e+06 Fmax= 3.66197e+03, atom= 4032 Step=2, Dmax= 5.0e-03 nm, Epot= -5.01438e+06 Fmax= 2.17491e+04, atom= 4032 Step=3, Dmax= 6.0e-03 nm, Epot= -5.01456e+06 Fmax= 9.13099e+03, atom= 4032 Step=5, Dmax= 3.6e-03 nm, Epot= -5.01468e+06 Fmax= 9.44298e+03, atom= 4032 Step= 10, Dmax= 2.7e-04 nm, Epot= -5.01470e+06 Fmax= 8.04093e+03, atom= 4032 Step= 11, Dmax= 3.2e-04 nm, Epot= -5.01472e+06 Fmax= 6.36864e+03, atom= 4032 Step= 12, Dmax= 3.9e-04 nm, Epot= -5.01474e+06 Fmax= 4.35105e+03, atom= 4032 Step= 14, Dmax= 2.3e-04 nm, Epot= -5.01476e+06 Fmax= 3.13319e+03, atom= 4032 Step= 16, Dmax= 1.4e-04 nm, Epot= -5.01478e+06 Fmax= 2.39737e+03, atom= 4032 Step= 18, Dmax= 8.4e-05 nm, Epot= -5.01478e+06 Fmax= 1.98224e+03, atom= 4032 Step= 21, Dmax= 2.5e-05 nm, Epot= -5.01479e+06 Fmax= 1.88313e+03, atom= 4034 Step= 22, Dmax= 3.0e-05 nm, Epot= -5.01479e+06 Fmax= 1.68824e+03, atom= 4032 Step= 23, Dmax= 3.6e-05 nm, Epot= -5.01479e+06 Fmax= 1.50693e+03, atom= 4032 Step= 25, Dmax= 2.2e-05 nm, Epot= -5.01479e+06 Fmax= 1.39532e+03, atom= 4032 Step= 26, Dmax= 2.6e-05 nm, Epot= -5.01480e+06 Fmax= 1.30313e+03, atom= 4032 Step= 27, Dmax= 3.1e-05 nm, Epot= -5.01481e+06 Fmax= 1.12668e+03, atom= 4034 Step= 28, Dmax= 3.8e-05 nm, Epot= -5.01482e+06 Fmax= 9.41676e+02, atom= 4034 Step= 30, Dmax= 2.3e-05 nm, Epot= -5.01483e+06 Fmax= 8.67996e+02, atom= 4032 Step= 31, Dmax= 2.7e-05 nm, Epot= -5.01483e+06 Fmax= 6.80316e+02, atom= 4034 Step= 32, Dmax= 3.2e-05 nm, Epot= -5.01484e+06 Fmax= 5.66923e+02, atom= 4034 Step= 33, Dmax= 3.9e-05 nm, Epot= -5.01485e+06 Fmax= 3.30411e+02, atom= 1881 Step= 35, Dmax= 2.3e-05 nm, Epot= -5.01487e+06 Fmax= 3.12606e+02, atom= 1881 Step= 37, Dmax= 1.4e-05 nm, Epot= -5.01488e+06 Fmax= 3.86990e+02, atom= 92925 Step= 38, Dmax= 1.7e-05 nm, Epot= -5.01489e+06 Fmax= 3.70596e+02, atom= 286823 Step= 40, Dmax= 1.0e-05 nm, Epot= -5.01489e+06 Fmax= 4.65471e+02, atom= 142601 Step= 41, Dmax= 1.2e-05 nm, Epot= -5.01490e+06 Fmax= 4.51394e+02, atom= 155810 Step= 43, Dmax= 7.3e-06 nm, Epot= -5.01490e+06 Fmax= 6.46500e+02, atom= 167601 Step= 47, Dmax= 1.1e-06 nm, Epot= -5.01490e+06 Fmax= 4.30994e+03, atom= 214498 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up traj.trr to ./#traj.trr.12# Back Off! I just backed up md.pdb to ./#md.pdb.8# Steepest Descents converged to machine precision in 48 steps, but did not reach the requested Fmax < 10. Potential Energy = -5.0149030e+06 Maximum force = 6.4650037e+02 on atom 167601 Norm of force = 7.3590344e+04 Kindly help me in this regard.I am attaching md.mdp file in which i have made the changes. -- akalabya N.I.T.Rourkela md.mdp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the reson for neutralizing the charge
hazizian wrote: Hi my ligand is Arginine (so it is not neccessary to use PRODRG )and the OPLS forcefield of gromacs make the itp file of it. I check and all the atoms present in the ligand itp file.There is no missing atom in the file. atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_287 1ARG N 1 -0.314.0067 ; qtot -0.3 2 opls_290 1ARG H1 1 0.33 1.008 ; qtot 0.03 3 opls_290 1ARG H2 1 0.33 1.008 ; qtot 0.36 4 opls_290 1ARG H3 1 0.33 1.008 ; qtot 0.69 5 opls_283 1ARG CA 1 0.04 12.011 ; qtot 0.73 6 opls_140 1ARG HA 1 0.06 1.008 ; qtot 0.79 7 opls_136 1ARG CB 2 -0.12 12.011 ; qtot 0.67 8 opls_140 1ARGHB1 2 0.06 1.008 ; qtot 0.73 9 opls_140 1ARGHB2 2 0.06 1.008 ; qtot 0.79 10 opls_308 1ARG CG 3 -0.05 12.011 ; qtot 0.74 11 opls_140 1ARGHG1 3 0.06 1.008 ; qtot 0.8 12 opls_140 1ARGHG2 3 0.06 1.008 ; qtot 0.86 13 opls_307 1ARG CD 4 0.19 12.011 ; qtot 1.05 14 opls_140 1ARGHD1 4 0.06 1.008 ; qtot 1.11 15 opls_140 1ARGHD2 4 0.06 1.008 ; qtot 1.17 16 opls_303 1ARG NE 5 -0.714.0067 ; qtot 0.47 17 opls_304 1ARG HE 5 0.44 1.008 ; qtot 0.91 18 opls_302 1ARG CZ 5 0.64 12.011 ; qtot 1.55 19 opls_300 1ARGNH1 6 -0.814.0067 ; qtot 0.75 20 opls_301 1ARG HH11 6 0.46 1.008 ; qtot 1.21 21 opls_301 1ARG HH12 6 0.46 1.008 ; qtot 1.67 22 opls_300 1ARGNH2 7 -0.814.0067 ; qtot 0.87 23 opls_301 1ARG HH21 7 0.46 1.008 ; qtot 1.33 24 opls_301 1ARG HH22 7 0.46 1.008 ; qtot 1.79 25 opls_271 1ARG C 80.7 12.011 ; qtot 2.49 26 opls_272 1ARG O1 8 -0.815.9994 ; qtot 1.69 27 opls_272 1ARG O2 8 -0.815.9994 ; qtot 0.89 So for neutralizing I break 0.11 charge to 8 number of 0.01 charge and 6 number of 0.005 cherge and add them to 8+3=11 H atoms. so the total charge of my ligand is +1.Is it correct way to solve this problem in the case that I could not find any missing atom in ligand topology file? No. When using pdb2gmx, how did you specify the N- and C-termini? Did you just indicate NH3+ and COO-? If so, this is incorrect. You have to use the zwitterionic options (since you are indeed dealing with a zwitterion). The broken charge comes from this mistake. If you ever find yourself with a fractional charge, do not get creative about how to interpret it. -Justin Tehran University of Medical Sciences www.tums.ac.ir -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the reson for neutralizing the charge
Hi my ligand is Arginine (so it is not neccessary to use PRODRG )and the OPLS forcefield of gromacs make the itp file of it. I check and all the atoms present in the ligand itp file.There is no missing atom in the file. atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_287 1ARG N 1 -0.314.0067 ; qtot -0.3 2 opls_290 1ARG H1 1 0.33 1.008 ; qtot 0.03 3 opls_290 1ARG H2 1 0.33 1.008 ; qtot 0.36 4 opls_290 1ARG H3 1 0.33 1.008 ; qtot 0.69 5 opls_283 1ARG CA 1 0.04 12.011 ; qtot 0.73 6 opls_140 1ARG HA 1 0.06 1.008 ; qtot 0.79 7 opls_136 1ARG CB 2 -0.12 12.011 ; qtot 0.67 8 opls_140 1ARGHB1 2 0.06 1.008 ; qtot 0.73 9 opls_140 1ARGHB2 2 0.06 1.008 ; qtot 0.79 10 opls_308 1ARG CG 3 -0.05 12.011 ; qtot 0.74 11 opls_140 1ARGHG1 3 0.06 1.008 ; qtot 0.8 12 opls_140 1ARGHG2 3 0.06 1.008 ; qtot 0.86 13 opls_307 1ARG CD 4 0.19 12.011 ; qtot 1.05 14 opls_140 1ARGHD1 4 0.06 1.008 ; qtot 1.11 15 opls_140 1ARGHD2 4 0.06 1.008 ; qtot 1.17 16 opls_303 1ARG NE 5 -0.714.0067 ; qtot 0.47 17 opls_304 1ARG HE 5 0.44 1.008 ; qtot 0.91 18 opls_302 1ARG CZ 5 0.64 12.011 ; qtot 1.55 19 opls_300 1ARGNH1 6 -0.814.0067 ; qtot 0.75 20 opls_301 1ARG HH11 6 0.46 1.008 ; qtot 1.21 21 opls_301 1ARG HH12 6 0.46 1.008 ; qtot 1.67 22 opls_300 1ARGNH2 7 -0.814.0067 ; qtot 0.87 23 opls_301 1ARG HH21 7 0.46 1.008 ; qtot 1.33 24 opls_301 1ARG HH22 7 0.46 1.008 ; qtot 1.79 25 opls_271 1ARG C 80.7 12.011 ; qtot 2.49 26 opls_272 1ARG O1 8 -0.815.9994 ; qtot 1.69 27 opls_272 1ARG O2 8 -0.815.9994 ; qtot 0.89 So for neutralizing I break 0.11 charge to 8 number of 0.01 charge and 6 number of 0.005 cherge and add them to 8+3=11 H atoms. so the total charge of my ligand is +1.Is it correct way to solve this problem in the case that I could not find any missing atom in ligand topology file? Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp error in simulation of membrane protein.
nitu sharma wrote: Hello justin , thanks for ur previous suggestion . I am doing simulation of membrene protein , as u suggest in previous mail to use gromos9653a6 forcefield parameters in topology file of protein+lipid bilayer. I have made topology accordingly like this- ; Include forcefield parameters #include "ffG53a6.itp" #include "lipid.itp" #include "dmpc.itp" As I have said, time and time again, the above setup will likely give problems. What you should do is append the relevant directives from lipid.itp into ffG53a6nb.itp and ffG53a6bon.itp, removing the section called ";; parameters for lipid-GROMOS interactions," as they pertain to ffgmx. [ molecules ] ; compound #mols Protein_A1 Protein_B1 DMPC128 SOL3552 Na 1 This isn't going to work either, since Na corresponds to an ffgmx NA+ ion; you need NA+, which is the correct nomenclature for ffG53a6. But when I run the grompp command I got the error like this- Fatal error: Atomtype CA not found Again, this is an ffgmx atom type, probably because you're using this hacked topology; including lipid.itp as is calls some ffgmx atom types. -Justin I have tried to solve this problem by adding CA atom with its mass in ffG53a6.atp file and atom CA with its all information ffG53a6nb.itp file but even after doing this correction I am getting same error . Please Can u suggest me what should I have to do to solve this problem . I am a new gromacs user , I have done the simulation of protein and lipid bilayer separetly but this type of problem didnot came so I have no much idea . I am waiting for ur reply. NITU SHARMA SCHOOL OF LIFE SCIENCES JAWAHERLAL NEHRU UNIVERSITY NEW DELHI, INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem
Hi, search in config.log for the compiler error. This should tell you the problem. If not post the compiler error. Roland On Tue, Apr 7, 2009 at 5:20 AM, Hongyan Xiao wrote: >Dear gmx-users, > > When I parallel install gromacs-4.0.4 using my own usr. I encountered the > problem. The following is my installation steps. > > Step 1: install lam-7.1.4 > $ cd lam-7.1.4 > $ ./configure --prefix=/home/xhy/software/lam-7.1.4 --without-fc > --with-rsh=ssh-x > $ make > $ make install > then adding /home/xhy/software/lam-7.1.4/bin into .bashrc file. > $ source .bashrc > > Step 2: install fftw-3.1.2 > $ cd fftw-3.1.2 > $ ./configure --prefix=/home/xhy/software/fftw-3.1.2 > --enable-float --enable-threads > $ make > $ make install > then adding /home/xhy/software/fftw-3.1.2/bin, > export > CPPFLAGS==-I/home/xhy/software/fftw-3.1.2/include and > export LDFLAGS=-L/home/xhy/software/fftw-3.1.2/lib into > .bashrc file. > $ source .bashrc > > Step 3: install gromacs-4.0.4 >$ cd gromacs-4.0.4 >$./configure --prefix=/home/xhy/software/gromacs-4.0.4 > --exec-prefix=/home/xhy/software/gromacs-4.0.4 --enable-mpi --with-fftw3 > --program-suffix=_mpi > > then I encountered the following errors: > > checking build system type... x86_64-unknown-linux-gnu > checking host system type... x86_64-unknown-linux-gnu > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for a thread-safe mkdir -p... /bin/mkdir -p > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking how to create a ustar tar archive... gnutar > checking for cc... cc > checking for C compiler default output file name... > configure: error: C compiler cannot create executables > See `config.log' for more details. > > Can you help me? I hope for your answer. Thank you very much! > > H.Y. Xiao > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp error in simulation of membrane protein.
Hello justin , thanks for ur previous suggestion . I am doing simulation of membrene protein , as u suggest in previous mail to use gromos9653a6 forcefield parameters in topology file of protein+lipid bilayer. I have made topology accordingly like this- ; Include forcefield parameters #include "ffG53a6.itp" #include "lipid.itp" #include "dmpc.itp" ; Include chain topologies #include "rr1_A.itp" #include "rr1_B.itp" ; Include position restrain protein ;#ifdef POSRES_PROTEIN ;#include "posre_A.itp" ;#include "posre_B.itp" ;#endif ; Include position restrain lipid ;#ifdef POSRES_LIPID ;#include "lip_posre.itp ;#endif ; Include water topology #ifdef FLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif #ifdef POSRES_WATER ;Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name PROTEIN IN DMPC BILAYER + WATER [ molecules ] ; compound #mols Protein_A1 Protein_B1 DMPC128 SOL3552 Na 1 But when I run the grompp command I got the error like this- Fatal error: Atomtype CA not found I have tried to solve this problem by adding CA atom with its mass in ffG53a6.atp file and atom CA with its all information ffG53a6nb.itp file but even after doing this correction I am getting same error . Please Can u suggest me what should I have to do to solve this problem . I am a new gromacs user , I have done the simulation of protein and lipid bilayer separetly but this type of problem didnot came so I have no much idea . I am waiting for ur reply. NITU SHARMA SCHOOL OF LIFE SCIENCES JAWAHERLAL NEHRU UNIVERSITY NEW DELHI, INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] install problem
Dear gmx-users, When I parallel install gromacs-4.0.4 using my own usr. I encountered the problem. The following is my installation steps. Step 1: install lam-7.1.4 $ cd lam-7.1.4 $ ./configure --prefix=/home/xhy/software/lam-7.1.4 --without-fc --with-rsh=ssh-x $ make $ make install then adding /home/xhy/software/lam-7.1.4/bin into .bashrc file. $ source .bashrc Step 2: install fftw-3.1.2 $ cd fftw-3.1.2 $ ./configure --prefix=/home/xhy/software/fftw-3.1.2 --enable-float --enable-threads $ make $ make install then adding /home/xhy/software/fftw-3.1.2/bin, export CPPFLAGS==-I/home/xhy/software/fftw-3.1.2/include and export LDFLAGS=-L/home/xhy/software/fftw-3.1.2/lib into .bashrc file. $ source .bashrc Step 3: install gromacs-4.0.4 $ cd gromacs-4.0.4 $./configure --prefix=/home/xhy/software/gromacs-4.0.4 --exec-prefix=/home/xhy/software/gromacs-4.0.4 --enable-mpi --with-fftw3 --program-suffix=_mpi then I encountered the following errors: checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... configure: error: C compiler cannot create executables See `config.log' for more details. Can you help me? I hope for your answer. Thank you very much! H.Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] the reson for neutralizing the charge
Hi, The issue here is not so much net neutrality of the whole system (although there can be important reasons for wanted this), but that your system has a small fractional charge. This indicates that there a probably missing atoms, probably in your ligand. That is a serious problem which you should fix. Check if all atoms in your ligand are present in the topology file. Berk > Date: Tue, 7 Apr 2009 17:16:19 +1000 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] the reson for neutralizing the charge > > Homa Azizian wrote: > > Hi > > I have a basic question about the charge. why is it important to neutralize > > the charge of ligand-protein complex. Is it true by neutralizing the tatal > > charge of ligand-protein complex we prevent the electrostatic intraction of > > ligand and protein? > > Any suggestion would be appreciated. > > Physical systems are normally neutral - cells have to do work to > maintain ion and/or charge imbalances. > > Physical models were normally parameterized under neutral conditions - > but you should check the literature for your force field. > > Some algorithms might be doubtful under non-neutral conditions - I'm not > sure whether Ewald methods are well-formed in such cases. Most > derivations I've seen seem to require it. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sdf
Dear gmax user I want to use G_SDF command. But the description of this comand is alittle bit complicate for me. I want to compute the density of water around protein and I dont know could I do it or not. I will be thankful if somebody suggest me by this command. Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer
Pawan Kumar wrote: Hello Sir, Can you please tell me how to couple ions with SOL ? Is there any command in gromacs to do that ? You need to define a group with SOL and the ions in an index file. This is uses as input to grompp so that it can make sense of the same group name when used in the .mdp file. See http://wiki.gromacs.org/index.php/Index_File Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] partial charge on protein
Homa Azizian wrote: Hi Justin and all when I do this command: pdb2gmx -ignh -f .pdb -o .pdb -water spce with OPLS force field. it seems that the protein has the charge of -3, while the ligand has the charge of 0.890 and finally it prints that the final charge is -2.11. I neutralized this charge with 2 NA+ so -0.11 charge remain (sorry for my mistake this is 0.11 not 0.08). So you should go and look at this ligand's topology and see where the charge is going wrong. The partial charges should at least vaguely correlate with chemical intuition. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the reson for neutralizing the charge
Homa Azizian wrote: Hi I have a basic question about the charge. why is it important to neutralize the charge of ligand-protein complex. Is it true by neutralizing the tatal charge of ligand-protein complex we prevent the electrostatic intraction of ligand and protein? Any suggestion would be appreciated. Physical systems are normally neutral - cells have to do work to maintain ion and/or charge imbalances. Physical models were normally parameterized under neutral conditions - but you should check the literature for your force field. Some algorithms might be doubtful under non-neutral conditions - I'm not sure whether Ewald methods are well-formed in such cases. Most derivations I've seen seem to require it. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
