<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>2 apr 2012 kl. 11.27 skrev ankita oindrila:</div><br class="Apple-interchange-newline"><blockquote type="cite"><u>We are trying to do simulation of lysozyme in water.</u><br><br>step with problem : energy minimization.<br><br>command given: <b style="color:rgb(255,0,0)">[root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr</b><br>
<br> :-) G R O M A C S (-:<br><br> Getting the Right Output Means no Artefacts in Calculating Stuff<br><br> :-) VERSION 4.0.5 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2008, The GROMACS development team,<br> check out <a href="http://www.gromacs.org/">http://www.gromacs.org</a> for more information.<br>
<br> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.<br><br> :-) grompp (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br>
-f minim.mdp Input, Opt! grompp input file with MD parameters<br> -po mdout.mdp Output grompp input file with MD parameters<br> -c 1AKI_solv_ions.gro Input Structure file: gro g96 pdb tpr tpb tpa<br>
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br> -n index.ndx Input, Opt. Index file<br> -p topol.top Input Topology file<br>
-pp processed.top Output, Opt. Topology file<br> -o em.tpr Output Run input file: tpr tpb tpa<br> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br> -e ener.edr Input, Opt. Energy file: edr ene<br>
<br>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-nice int 0 Set the nicelevel<br>-[no]v bool yes Be loud and noisy<br>
-time real -1 Take frame at or first after this time.<br>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br> sites<br>-maxwarn int 0 Number of allowed warnings during input processing<br>
-[no]zero bool no Set parameters for bonded interactions without<br> defaults to zero instead of generating an error<br>-[no]renum bool yes Renumber atomtypes and minimize number of<br>
atomtypes<br><br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#<br>checking input for internal consistency...<br>processing topology...<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp<br>
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp<br>Generated 332520 of the 332520 non-bonded parameter combinations<br>
Generating 1-4 interactions: fudge = 0.5<br>Generated 332520 of the 332520 1-4 parameter combinations<br>Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp<br>
Excluding 3 bonded neighbours molecule type 'Protein_A'<br>Excluding 2 bonded neighbours molecule type 'SOL'<br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.0.5<br>
Source code file: toppush.c, line: 1641<br><br><b style="color:rgb(255,0,0)">Fatal error:<br>No such moleculetype NA</b><br><br>what should we do????<br></blockquote><div><br></div><div>Have a look at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></div><div><br></div><br><blockquote type="cite"><br>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div>
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