[gmx-users] Error running grompp
Dear gmx users: I m carrying a protein explicit solvent simulation using gromacs 3.3, then i added water, but in next step, I m getting the following error, grompp -f em.mdp -c try.gro -p A.top -o A_em.tpr :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -ctry.gro InputGeneric structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -deshuf deshuf.ndx Output, Opt. Index file -p A.top InputTopology file -pp processed.top Output, Opt. Topology file -o A_em.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 0 Set the nicelevel -[no]v boolyes Be loud and noisy -time real -1 Take frame at or first after this time. -npint 1 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds boolyes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarnint 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum boolyes Renumber atomtypes and minimize number of atomtypes creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations Cleaning up temporary file grompp3wF5if --- Program grompp, VERSION 3.3.1 Source code file: toputil.c, line: 61 Fatal error: Atomtype 'C3' not found! --- "Baby, It Aint Over Till It's Over" (Lenny Kravitz) Can you tell me how to correct it? Best Regards! Fufeng liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Regarding Na ions
> Dear gmx users, > I am thankful to Dr.Mark and Dr.Osmair for > their responce to my queries. As per their suggestion, > I checked ions.itp file in that sodium atoms are > represented by NA+ in opls force field. I am using > gromacs 3.3.1 version. > > > Step 32, time 0.064 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 0.002582 (between atoms 5262 and 5310) rms > 0.38 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint > length >5262 5310 31.20.1000 0.0997 0.1000 > > Step 33, time 0.066 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 0.003343 (between atoms 5262 and 5310) rms > 0.57 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint > length >5368 5416 69.40.0999 0.1001 0.1000 > > Step 34, time 0.068 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 0.005428 (between atoms 5262 and 5310) rms > 0.76 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint > length >5262 5310 67.90.1003 0.0995 0.1000 >5368 5416 47.00.1001 0.1002 0.1000 > > Step 35, time 0.07 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 0.002371 (between atoms 5368 and 5416) rms > 0.36 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint > length >5262 5310 43.40.0995 0.1002 0.1000 >5368 5416 40.90.1002 0.0998 0.1000 > > > Can you tell where I have done mistake. > Any suggestion is appreciated. Please read http://wiki.gromacs.org/index.php/Blowing_Up and check that you've followed the advice here http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Regarding Na ions
Dear gmx users, I am thankful to Dr.Mark and Dr.Osmair for their responce to my queries. As per their suggestion, I checked ions.itp file in that sodium atoms are represented by NA+ in opls force field. I am using gromacs 3.3.1 version. [moleculetype ] ; molname nrexcl NA+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 opls_4071 NA+ NA 1 1 22.98977 As per Dr.Osmair suggestion, I built a sodium.itp file, the file was shown below. Z [ moleculetype ] ; NAmenrexcl NA+1 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_407 1NA+ NA 1 122.9898 ; qtot 1 2 opls_407 2NA+ NA 2 122.9898 ; qtot 2 3 opls_407 3NA+ NA 3 122.9898 ; qtot 3 4 opls_407 4NA+ NA 4 122.9898 ; qtot 4 5 opls_407 5NA+ NA 5 122.9898 ; qtot 5 6 opls_407 6NA+ NA 6 122.9898 ; qtot 6 7 opls_407 7NA+ NA 7 122.9898 ; qtot 7 8 opls_407 8NA+ NA 8 122.9898 ; qtot 8 9 opls_407 9NA+ NA 9 122.9898 ; qtot 9 10 opls_407 10NA+ NA 10 122.9898 ; qtot 10 11 opls_407 11NA+ NA 11 122.9898 ; qtot 11 12 opls_407 12NA+ NA 12 122.9898 ; qtot 12 . .. .. and also tried with the fallowing type... [ moleculetype ] ; Namenrexcl Sodium1 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_405 1Na Na 1 135.4530 ; qtot 1 2 opls_405 2Na Na 2 135.4530 ; qtot 2 3 opls_405 3Na Na 3 135.4530 ; qtot 3 4 opls_405 4Na Na 4 135.4530 ; qtot 4 5 opls_405 5Na Na 5 135.4530 ; qtot 5 6 opls_405 6Na Na 6 135.4530 ; qtot 6 7 opls_405 7Na Na 7 135.4530 ; qtot 7 8 opls_405 8Na Na 8 135.4530 ; qtot 8 9 opls_405 9Na Na 9 135.4530 ; qtot 9 . . . ZZZ When i run grompp command to prepare bilater-ions.tpr file, I couldn't observe any error message and shown below. processing topology... Generated 345696 of the 345696 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 345606 of the 345696 1-4 parameter combinations Excluding 3 bonded neighbours for POPE 96 turning all bonds into constraints... Excluding 3 bonded neighbours for DPOP 32 turning all bonds into constraints... Excluding 2 bonded neighbours for SOL 3909 turning all bonds into constraints... Excluding 1 bonded neighbours for NA+ 1 turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 303 K renumbering atomtypes... converting bonded parameters... # ANGLES: 7520 # PDIHS: 3424 # RBDIHS: 2944 # IDIHS: 544 # LJ14: 3680 # CONSTR: 6560 # SETTLE: 3909 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Making dummy/rest group for Acceleration containing 18447 elements Making dummy/rest group for Freeze containing 18447 elements Making dummy/rest group for Energy Mon. containing 18447 elements Making dummy/rest group for VCM containing 18447 elements Number of degrees of freedom in T-Coupling group POP is 10079.18 Number of degrees of freedom in T-Coupling group DPO is 3423.72 Number of degrees of freedom in T-Coupling group SOL is 23452.10 Number of degrees of freedom in T-Coupling group NA+ is 95.99 Making dummy/rest group for User1 containing 18447 elements Making dummy/rest group for User2 containing 18447 elements Making dummy/rest group for XTC containing 18447 elements Making dummy/rest group for Or. Res. Fit containing 18447 elements Making dummy/rest group for QMMM containing 18447 elements T-Coupling has 4 element(s): POP DPO SOL NA+ Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 e
Re: [gmx-users] Error durign Grompp
> Dear gmx users: > I m carrying a protein explicit solvent simulation using gromacs > 3.3, > then i added water, but in next step, I m getting the following error, > > grompp -f em.mdp -c try.gro -p A.top -o A_em.tpr > --- > Program grompp, VERSION 3.3.1 > Source code file: toputil.c, line: 61 > > Fatal error: > Atomtype 'C3' not found! > --- This mailing list is not a substitute for thinking. Here grompp is telling you that it didn't find atomtype C3... so work out where it is being used and whether or not that's a good thing. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re:Error_message
dos2unix is always a good companion. Regards, Yang Ye - Original Message From: pkmukher <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Friday, July 6, 2007 10:13:02 AM Subject: [gmx-users] Re:Error_message Chris, Thanks for your suggestion. I was downloading the .mdp file in a windows machine and then moving it to the cluster. I moved using the binary format instead of the ASCII and it worked. probably it was inserting some carriage return or other charecters. Thanks once again Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error durign Grompp
Dear gmx users: I m carrying a protein explicit solvent simulation using gromacs 3.3, then i added water, but in next step, I m getting the following error, grompp -f em.mdp -c try.gro -p A.top -o A_em.tpr :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -ctry.gro InputGeneric structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -deshuf deshuf.ndx Output, Opt. Index file -p A.top InputTopology file -pp processed.top Output, Opt. Topology file -o A_em.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 0 Set the nicelevel -[no]v boolyes Be loud and noisy -time real -1 Take frame at or first after this time. -npint 1 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds boolyes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarnint 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum boolyes Renumber atomtypes and minimize number of atomtypes creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations Cleaning up temporary file grompp3wF5if --- Program grompp, VERSION 3.3.1 Source code file: toputil.c, line: 61 Fatal error: Atomtype 'C3' not found! --- "Baby, It Aint Over Till It's Over" (Lenny Kravitz) Can you tell me how to correct it? Best Regards! Fufeng liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:Error_message
Chris, Thanks for your suggestion. I was downloading the .mdp file in a windows machine and then moving it to the cluster. I moved using the binary format instead of the ASCII and it worked. probably it was inserting some carriage return or other charecters. Thanks once again Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error_message
define = -DFLEX_SPC ; Use Fergusons Flexible water model [5]
That is not something that I am familiar with. Could you be including a
corrupted section of .itp? It's not clear to me why
that would cause the problem that you outline here, but it's a place to start.
Also is your .mdp file in dos format?
To debug this, start with this:
touch empty.mdp
grompp -f empty.mdp
cp mdout.mdp correct.mdp
{edit correct.mdp values one at a time, e.g. change integrator from md to steep}
grompp -f correct.mdp ...
If that works, then try to figure out what the problem was.
Also, you can try adding in the options that you are having difficulty with one
at a time to an otherwise empty mdp file.
Also, please make the title more descriptive next time you start a post.
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Re: [gmx-users] Nanotubes with Tubegen
Christopher Stiles wrote: I am trying to do a simulation involving a SWCNT generated by Tubegen (http://turin.nss.udel.edu/research/tubegenonline.html) . Then I use Chimera to add hydrogen to the end carbon atoms (I did this because it was given as a possible solution in of the articles I ran across, although I have tried it both with hydrogen and without resulting in the same outcome). And I got testH.pdb from this… I tryed to run pdb2gmx using the following command: pdb2gmx -f testH.pdb -p testH.top -o testH.gro I get the following error when selecting 1: GROMOS96 43b1 vacuum force field: Program pdb2gmx, VERSION 3.3.1 Source code file: resall.c, line: 438 Fatal error: Residue 'UNK' not found in residue topology database Then if I try to use x2top instead using the following command: I get the following error when selecting 1: GROMOS96 43b1 vacuum force field: Program x2top, VERSION 3.3.1 Source code file: futil.c, line: 537 Fatal error: Library file ffG43b1.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) In my library there only exists one file with a n2t extension and it is ffgmx.n2t and did you try this one? So well I have spent countless hours reading and looking through the entirety web resources to no avail. So I am hoping for a hand to point me in the correct direction. Thank you very much for your help! ~Christopher Stiles College of Nanoscale Science and Engineering (CNSE) State University of New York, Albany, New York 12203, USA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Nanotubes with Tubegen
I am trying to do a simulation involving a SWCNT generated by Tubegen (http://turin.nss.udel.edu/research/tubegenonline.html) . Then I use Chimera to add hydrogen to the end carbon atoms (I did this because it was given as a possible solution in of the articles I ran across, although I have tried it both with hydrogen and without resulting in the same outcome). And I got testH.pdb from this. I tryed to run pdb2gmx using the following command: pdb2gmx -f testH.pdb -p testH.top -o testH.gro I get the following error when selecting 1: GROMOS96 43b1 vacuum force field: Program pdb2gmx, VERSION 3.3.1 Source code file: resall.c, line: 438 Fatal error: Residue 'UNK' not found in residue topology database Then if I try to use x2top instead using the following command: I get the following error when selecting 1: GROMOS96 43b1 vacuum force field: Program x2top, VERSION 3.3.1 Source code file: futil.c, line: 537 Fatal error: Library file ffG43b1.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) In my library there only exists one file with a n2t extension and it is ffgmx.n2t So well I have spent countless hours reading and looking through the entirety web resources to no avail. So I am hoping for a hand to point me in the correct direction. Thank you very much for your help! ~Christopher Stiles College of Nanoscale Science and Engineering (CNSE) State University of New York, Albany, New York 12203, USA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error_message
Dr. Spoel, Thanks for your reply. It seems that the program raises 4 exceptions while writing a statusfile in regards to 4 variables (integrator,ns-type, optimize_fft, constraints) in the .mdp file. In all cases one of the possible options for each variable is given in the input .mdp file.However the program is not reading it. Is this a syntax or spacing problem. Following is the COMPLTE error message and the .mdp file I am using. [EMAIL PROTECTED]:~/gromacs/drugenz2/junk/junk2> grompp -f em.mdp -c trp2.pdb -p trp.top -o trpjunk.tpr :-) G R O M A C S (-: GROtesk MACabre and Sinister :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -f em.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c trp2.pdb InputGeneric structure: gro g96 pdb tpr tpb tpa xml -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml -n index.ndx Input, Opt. Index file -deshuf deshuf.ndx Output, Opt. Index file -ptrp.top InputTopology file -pp processed.top Output, Opt. Topology file -otrpjunk.tpr Output Generic run input: tpr tpb tpa xml -t traj.trr Input, Opt. Full precision trajectory: trr trj -e ener.edr Input, Opt. Generic energy: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint 0 Set the nicelevel -[no]v boolyes Be loud and noisy -time real -1 Take frame at or first after this time. -npint 1 Generate statusfile for # nodes -[no]shuffle bool no Shuffle molecules over nodes -[no]sort bool no Sort molecules according to X coordinate -[no]rmvsbds boolyes Remove constant bonded interactions with virtual sites -load string Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node -maxwarnint 10 Number of warnings after which input processing stops -[no]check14 bool no Remove 1-4 interactions without Van der Waals -[no]renum boolyes Renumber atomtypes and minimize number of atomtypes creating statusfile for 1 node... ' for variable integrator, using 'md' Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi' ' for variable ns-type, using 'Grid' Next time use one of: 'Grid' 'Simple' ' for variable optimize_fft, using 'no' Next time use one of: 'no' 'yes' ' for variable constraints, using 'none' Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles' checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 NOTE: System has non-zero total charge: 7.02e+00 processing coordinates... double-checking input for internal consistency... --- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 1109 Fatal error: There were 4 error(s) processing your input --- "Whatever Happened to Pong ?" (F. Black) ### [EMAIL PROTECTED]:~/gromacs/drugenz2/junk/junk2> more em.mdp title = drg_trp cpp = /usr/bin/cpp ; location of cpp on linux define = -DFLEX_SPC ; Use Fergusons Flexible water model [5] constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order
[gmx-users] g_enemat
Hi All I am trying to get the interaction free energy between a single solute and solvent to calculate the solvation free energy finally. For that, I ran a 10 ns trajectory of an NpT ensemble with two separate energy groups (solute and solvent). The output file from the g_enemat tool looked as following; ** # This file was created Thu Jul 5 10:42:39 2007 # by the following command: # g_enemat -f rerun.edr -groups groups.dat # # g_enemat is part of G R O M A C S: # # GROningen MAchine for Chemical Simulation # @title "Mean Energy" @xaxis label "Residue" @yaxis label "kJ/mol" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ legend string 0 "Coul-SR" @ legend string 1 "LJ-SR" @ legend string 2 "total" @ legend string 3 "Free" @ legend string 4 "Diff" @TYPE xy #grp Coul-SR LJ-SR total Free Diff 1-19973-33241-53214 inf 2-135.2-41506-41641 inf * Here I am having a little trouble in interpreting the results shown above. Since I am interested in the interaction energy between the two groups, I expected to get a single value for each different energy term. Instead I got values for two groups separately, and, furthermore, the value for the free energy was inf (might be inifite). Could someone help me how I can interpret the data? Or should I change some thing to get the right answer? Thank you in advance Sunjoo _ Microsoft 기술로 완성된 강력한 스팸 차단으로 원하는 메일만 깨끗하게, Windows Live Hotmail! http://mail.live.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Regarding Na ions
You can build a file, e.g. sodium.itp: [ moleculetype ] ; Namenrexcl sodium1 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_405 1 Na Na 1 1 35.453 ; qtot 1 2 opls_405 2 Na Na 2 1 35.453 ; qtot 2 2 opls_405 3 Na Na 3 1 35.453 ; qtot 2 . . . Osmair Brazil > > Dear gmx users, > > I am trying to neutralize lipid bilayer > > with Na ions by using genion command: > > genion -f bilayer.tpr -o bilayer-Na.pdb -np 32 -pname Na -pq 1 > > > > Here is my bilayer.top file > > #include "ffoplsaa.itp" > > #include "pope.itp" > > #include "dpopg.itp" > > #include "ions.itp" > > One of these ones should be defining a sodium ion moleculetype ... have a > look and see what it's called there! > > > [ molecules ] > > ; namenumber > > POPE 96 > > DPOP 32 > > SOL 3909 > > Na 32 > > > > I am getiing fallowing eror. > > x > > processing topology... > > Generated 344865 of the 344865 non-bonded parameter combinations > > Generating 1-4 interactions: fudge = 0.5 > > Generated 344775 of the 344865 1-4 parameter combinations > > Excluding 3 bonded neighbours for POPE 96 > > turning all bonds into constraints... > > Excluding 3 bonded neighbours for DPOP 32 > > turning all bonds into constraints... > > Excluding 2 bonded neighbours for SOL 3909 > > turning all bonds into constraints... > > Cleaning up temporary file gromppVHJgxO > > --- > > Program grompp, VERSION 3.3.1 > > Source code file: toppush.c, line: 1293 > > > > Fatal error: > > No such moleculetype Na > > xxx > > > > Would you tell me what files, i have to modify. Any suggestion is > > appreciated. > > Mark > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error_message
pkmukher wrote: Hi, I am trying to generate a .tpr file.I am getting the following error message (below). Fatal error: There were 4 error(s) processing your input I could not understand what the error(s) were since nothing else was given.Is there some place where the details of the error will be listed so that i can rectify them.Thanks Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 Excluding 3 bonded neighbours for IN4 1 Excluding 2 bonded neighbours for SOL 4778 NOTE: System has non-zero total charge: 9.02e+00 processing coordinates... double-checking input for internal consistency... --- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 1109 Fatal error: There were 4 error(s) processing your input --- "Encountered Subspace Anomaly" (Star Trek) Read the COMPLETE output from grompp and if you still don't understand the error send the COMPLETE output to the list. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Regarding Na ions
> Dear gmx users, > I am trying to neutralize lipid bilayer > with Na ions by using genion command: > genion -f bilayer.tpr -o bilayer-Na.pdb -np 32 -pname Na -pq 1 > > Here is my bilayer.top file > #include "ffoplsaa.itp" > #include "pope.itp" > #include "dpopg.itp" > #include "ions.itp" One of these ones should be defining a sodium ion moleculetype ... have a look and see what it's called there! > [ molecules ] > ; namenumber > POPE 96 > DPOP 32 > SOL 3909 > Na 32 > > I am getiing fallowing eror. > x > processing topology... > Generated 344865 of the 344865 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 344775 of the 344865 1-4 parameter combinations > Excluding 3 bonded neighbours for POPE 96 > turning all bonds into constraints... > Excluding 3 bonded neighbours for DPOP 32 > turning all bonds into constraints... > Excluding 2 bonded neighbours for SOL 3909 > turning all bonds into constraints... > Cleaning up temporary file gromppVHJgxO > --- > Program grompp, VERSION 3.3.1 > Source code file: toppush.c, line: 1293 > > Fatal error: > No such moleculetype Na > xxx > > Would you tell me what files, i have to modify. Any suggestion is > appreciated. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] get_index
Pedro Alexandre de Araújo Gomes Lapido Loureiro a écrit :
echo 3 4 5 6 7 | program
I said many index groups.
Even with hundreds of groups, this is quite trivial, you could use
something like :
make_ndx -f ini/${molecule}.gro \
-o ini/${molecule}.ndx &> ini/make_ndx.log
[gmx-users] Error_message
Hi, I am trying to generate a .tpr file.I am getting the following error message (below). Fatal error: There were 4 error(s) processing your input I could not understand what the error(s) were since nothing else was given.Is there some place where the details of the error will be listed so that i can rectify them.Thanks Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein 1 Excluding 3 bonded neighbours for IN4 1 Excluding 2 bonded neighbours for SOL 4778 NOTE: System has non-zero total charge: 9.02e+00 processing coordinates... double-checking input for internal consistency... --- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 1109 Fatal error: There were 4 error(s) processing your input --- "Encountered Subspace Anomaly" (Star Trek) Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Regarding Na ions
Dear gmx users, I am trying to neutralize lipid bilayer with Na ions by using genion command: genion -f bilayer.tpr -o bilayer-Na.pdb -np 32 -pname Na -pq 1 Here is my bilayer.top file #include "ffoplsaa.itp" #include "pope.itp" #include "dpopg.itp" #include "ions.itp" #ifdef FLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif [ system ] ; name Mixture of POPE and POPG lipid bilayer in 3:1 ratio [ molecules ] ; namenumber POPE 96 DPOP 32 SOL 3909 Na 32 I am getiing fallowing eror. x processing topology... Generated 344865 of the 344865 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 344775 of the 344865 1-4 parameter combinations Excluding 3 bonded neighbours for POPE 96 turning all bonds into constraints... Excluding 3 bonded neighbours for DPOP 32 turning all bonds into constraints... Excluding 2 bonded neighbours for SOL 3909 turning all bonds into constraints... Cleaning up temporary file gromppVHJgxO --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1293 Fatal error: No such moleculetype Na xxx Would you tell me what files, i have to modify. Any suggestion is appreciated. Thank you in advance. with regards, Nagaraju - Yahoo! oneSearch: Finally, mobile search that gives answers, not web links. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] get_index
Hmm, for what it's worth, I think the answer might be to dig into the routines for reading the index files itself. I think it will come down to calling init_index and rd_groups (src/gmxlib/index.c). Tsjerk On 7/5/07, Mark Abraham <[EMAIL PROTECTED]> wrote: >> >> echo 3 4 5 6 7 | program >> >> I said many index groups. Yeah, we're not stupid, but you're trying to get our help for free... so give us an example so that we know what's going on in your head! Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
