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 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
