<span class="gmail_quote"><br></span>
<div>Hi Guys,<br><br>Sorry for being sketchy on the details. I was trying to merge an unpolarised water topology file with a polarised one (sw3.itp....similar to sw.itp in gromacs). I am essentially repeating the Ribonuclease S -peptide tutorial in the "getting started" section of the gromacs website (but with polarisable water). When I preprocess the modified topology file (inorder to do energy minimization...em) in grompp
<strong>(</strong><font style="COLOR: rgb(0,0,0); FONT-FAMILY: arial,sans-serif" color="#ffffff"><strong>grompp -v -f em -c b4em -o em -p speptide) </strong>I get the following output<strong>:</strong></font></div>
<div><br> <em> :-) G R O M A C S (-:<br><br> S C A M O R G<br><br> :-) VERSION 3.3 (-:<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) 2001-2004, The GROMACS development team,<br> check out </em><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/" target="_blank">
<em>http://www.gromacs.org</em></a><em> 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> :-) /usr/local/gromacs/bin/grompp (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------
<br> -f em.mdp Input, Opt! grompp input file with MD parameters<br> -po mdout.mdp Output grompp input file with MD parameters<br> -c b4em.gro Input Generic structure: gro g96 pdb tpr tpb tpa
<br> xml<br> -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa<br> xml<br> -rb <span></span> conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
<br> xml<br> -n index.ndx Input, Opt. Index file<br>-deshuf deshuf.ndx Output, Opt. Index file<br> -p speptide.top Input Topology file<br> -pp processed.top Output, Opt. Topology file
<br> -o em.tpr Output Generic run input: tpr tpb tpa xml<br> -t traj.trr Input, Opt. Full precision trajectory: trr trj<br> -e ener.edr Input, Opt. Generic energy: 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> -np int 1 Generate statusfile for # nodes<br>-[no]shuffle bool no Shuffle molecules over nodes<br> -[no]sort bool no Sort molecules according to X coordinate<br>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
<br> sites<br> -load string Releative load capacity of each node on a<br> parallel machine. Be sure to use quotes around<br> the string, which should contain a number for
<br> each node<br> -maxwarn int 10 Number of warnings after which input processing<br> stops<br>-[no]check14 bool no Remove 1-4 interactions without Van der Waals
<br> -[no]renum bool yes Renumber atomtypes and minimize number of<br> atomtypes<br><br>creating statusfile for 1 node...<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.81#<br>
checking input for internal consistency...<br>calling /usr/bin/cpp...<br>processing topology...<br>Generated 279 of the 1225 non-bonded parameter combinations<span></span> <br>Cleaning up temporary file gromppaew5iO<br>-------------------------------------------------------
<br>Program grompp, VERSION 3.3<br>Source code file: toppush.c, line: 754<br><br>Fatal error:<br>Atoms in the .top are not numbered consecutively from 1</em></div>
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