2 apr 2012 kl. 16.02 skrev lina: > On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila <[email protected]> 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.
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 list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > 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 [email protected]. > 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 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
