Re:[gmx-users] Carbohydrate MD Simulation
Hi Nancy, I think that the atom C1 in residue TRP 1 does not exist in rtp entry. In other words, atom C1 is not understood by the software. You should change the atom type in order to be understood. I have a question, how do you obtain the URL about trehalose. Because I want to some polyols from PDB. Can you tell me how to obtain the pdb files about orginic molecules? Thanks a lot! Good luck! Fufeng Liu ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 difference about NPT and NVT ensemble.
Hello, everyone, I have some questions about ensemble. Would you please tell me about NPT or NVT ensemble? What difference about them? And how to define in the molecular dynamics mdp file? What ensemble does the below parameters extracted from my mdp file? ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Thank you for your kind consideration of these questions. Sincerely, 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to calculate the RMSD of the peptide conformation relative to the NMR structure?
Dear everyone, Can somebody tell me how to calculate the RMSD of the peptide conformation relative to the NMR structure? Thanks again! 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] How to analyse the number of atom around the protein?
Hi, I am trying to analyse the number of atom around the protein. For example, I want to calculate the number of oxygen atom of water within 3A of the protein. Can somebody tell me how to do it? Or tell me choose which commands to do it. Many thanks in advance, Fufengliu ___ 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] How compare the simulated structure of the same peptide to the NMR strucutre?
Hi, all I have simulated a beta-hairpin folded in explicit water, I want to compare the simulated structure to the experimental structure using NMR. Can you tell me how to do it? Thanks a lot! fufengliu ___ 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] How to simulate peptide capped with ACE?
Dear gromacs users, I trying to simulate a peptide capped with ACE, when I run grompp, I got the following error: WARNING 1 [file 1.top, line 306]: No default G96Angle types, using zeroes. I checked the topology and found the ACE group disappears. I think that the grompp doesn¡¯t handle correctly the ACE group. I had browsed to the mailing list archive and found lots of problems similar to mine, but I couldn¡¯t know how to solve it? Someone can tell me in detail how to do it? Thank you for your help. 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] 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
[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
