Dear All,<br><br>I am trying to do equilibration of 8M urea in gromacs 4.0 in a 3nm cubic box. I created posre.itp from genpr selecting only UREA atoms to be restrainted ( em.gro was used to generate this posre.itp)<br><br>
<i><b>The error message is given below :</b></i><br><br> grompp -f pr.mdp -c em3.gro -p sys.top -o pr.tpr<br><br> :-) G R O M A C S (-:<br><br> GROwing Monsters And Cloning Shrimps<br>
<br> :-) VERSION 4.0 (-:<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 pr.mdp Input, Opt! grompp input file with MD parameters<br>
-po mdout.mdp Output grompp input file with MD parameters<br> -c em3.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 sys.top Input Topology file<br> -pp processed.top Output, Opt. Topology file<br>
-o pr.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>Ignoring obsolete mdp entry 'cpp'<br>
<br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#<br>checking input for internal consistency...<br>processing topology...<br>Opening library file /usr/local/gromacs4/share/gromacs/top/ffG43a1.itp<br>Opening library file /usr/local/gromacs4/share/gromacs/top/ffG43a1nb.itp<br>
Opening library file /usr/local/gromacs4/share/gromacs/top/ffG43a1bon.itp<br>Opening library file /usr/local/gromacs4/share/gromacs/top/ff_dum.itp<br>Opening library file /usr/local/gromacs4/share/gromacs/top/spc.itp<br>Generated 279 of the 1225 non-bonded parameter combinations<br>
<br><b>-------------------------------------------------------<br>Program grompp, VERSION 4.0<br>Source code file: toppush.c, line: 1196<br><br>Fatal error:<br>[ file posre.itp, line 13 ]:<br>Atom index (9) in position_restraints out of bounds (1-8).<br>
This probably means that you have inserted topology section "position_restraints"<br>in a part belonging to a different molecule than you intended to.<br>In that case move the "position_restraints" section to the right molecule.<br>
-------------------------------------------------------<br></b><br><br><i><b>My top file is : </b></i><br><br>; This is your topology file<br>; UREA in Water t= 0.00000<br>;<br>; Include forcefield parameters<br>
#include "ffG43a1.itp"<br><br>#include "spc.itp"<br>#include "urea.itp"<br><br>; Include Position restraint file<br>#ifdef POSRES<br>#include "posre.itp"<br>#endif<br><br><br><br><br>
[ system ]<br>; Name<br>UREA in Water<br><br>[ molecules ]<br>; Compound #mols<br>UREA 130<br>SOL 1149<br><br><br><br>I <i>guess</i> the error is because position restraints for all the 130 urea molecules is not working but only for the first molecule of UREA. ( Hence out of bounds after 1-8.) <br>
<br>Can anyone please suggest a way out of this problem? i want to position restrain all the urea molecules. <br><br>Thank you all for time,<br><br>Regards,<br>Karan<br><br><br><br><br><br><br><br><br>