[gmx-users] em fatal error!
*We are trying to do simulation of lysozyme in water.* step with problem : energy minimization. command given: *[root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr* :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, 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 minim.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 1AKI_solv_ions.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p topol.top InputTopology file -pp processed.top Output, Opt. Topology file -o em.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 1641 *Fatal error: No such moleculetype NA* what should we do -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] em fatal error!
2 apr 2012 kl. 11.27 skrev ankita oindrila: We are trying to do simulation of lysozyme in water. step with problem : energy minimization. command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, 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 minim.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 1AKI_solv_ions.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p topol.top InputTopology file -pp processed.top Output, Opt. Topology file -o em.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype NA what should we do Have a look at http://www.gromacs.org/Documentation/Errors -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] em fatal error!
Hi Ankita , The error is self-explanatory , and simple to interpret it. You check the Topology file and see the last line that showing added ions ... What was your genion COMMAND LINE Have a nice day Rama On Mon, Apr 2, 2012 at 3:19 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 2 apr 2012 kl. 11.27 skrev ankita oindrila: We are trying to do simulation of lysozyme in water. step with problem : energy minimization. command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, 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 minim.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 1AKI_solv_ions.gro Input Structure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p topol.top Input Topology file -pp processed.top Output, Opt. Topology file -o em.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype NA what should we do Have a look at http://www.gromacs.org/Documentation/Errors -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] em fatal error!
Hi Ankita, command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr It is very unwise to run such things as root. By the way, if you follow a tutorial and refer to it, please send a link. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] em fatal error!
On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila oina...@gmail.com wrote: We are trying to do simulation of lysozyme in water. step with problem : energy minimization. command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, 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 minim.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 1AKI_solv_ions.gro Input Structure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p topol.top Input Topology file -pp processed.top Output, Opt. Topology file -o em.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]v bool yes Be loud and noisy -time real -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int 0 Number of allowed warnings during input processing -[no]zero bool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.0.5 You use Version 4.0.5. If I remember correctly, the earlier version has different pname. (seems one is NA+, one is NA) If I were you, I would update to latest version and try. Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype NA what should we do -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] em fatal error!
2 apr 2012 kl. 16.02 skrev lina: On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila oina...@gmail.com wrote: We are trying to do simulation of lysozyme in water. step with problem : energy minimization. command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr :-) G R O M A C S (-: Getting the Right Output Means no Artefacts in Calculating Stuff :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, 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 minim.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 1AKI_solv_ions.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p topol.top InputTopology file -pp processed.top Output, Opt. Topology file -o em.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.0.5 You use Version 4.0.5. If I remember correctly, the earlier version has different pname. (seems one is NA+, one is NA) If I were you, I would update to latest version and try. Upgrading may be a good thing for many reasons. To see what are the names of ions, check ions.itp. Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype NA what should we do -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755
