<div>Hi,</div>
<div> I am going to analyse the normal mode analysis of n-butane. For this I donloaded a PDB id .Then opened in wordpad and just took the glu residue.Opend it on viewerpro and deleted the -COO, NH2,-CH2 portion to make it n-butane.Then made a pdb file and ran in GROMACS. I suceesfully created the topology file and did the next steps .But grompp showed the following error</div>
<div><a href="mailto:abhijit@SCFBioServer">abhijit@SCFBioServer</a> project]$ grompp -v -f em.mdp -c ab.gro -p ab.top -o <a href="http://ab.tp">ab.tp</a> r<br>
:-) G R O M A C S (-:</div>
<div> GROwing Monsters And Cloning Shrimps</div>
<div> :-) VERSION 4.0.4 (-:</div>
<div><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.</div>
<div> 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.</div>
<div> :-) grompp (-:</div>
<div>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 ab.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 ab.top Input Topology file<br> -pp processed.top Output, Opt. Topology file<br> -o ab.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</div>
<div>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</div>
<div>Ignoring obsolete mdp entry 'cpp'</div>
<div>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9#<br>checking input for internal consistency...<br>processing topology...<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2nb.itp<br>
Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2bon.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp<br>Generated 380 of the 1326 non-bonded parameter combinations<br>Opening library file /usr/local/gromacs/share/gromacs/top/spc.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>Excluding 2 bonded neighbours molecule type 'SOL'</div>
<div>NOTE 1 [file ab.top, line 126]:<br> System has non-zero total charge: -1.000000e-00</div>
<div> </div>
<div>processing coordinates...</div>
<div>-------------------------------------------------------<br>Program grompp, VERSION 4.0.4<br>Source code file: grompp.c, line: 362</div>
<div>Fatal error:<br>number of coordinates in coordinate file (ab.gro, 13)<br> does not match topology (ab.top, 29602)<br>-------------------------------------------------------</div>
<div>"A Lady Shaves Her Legs" (C. Meijering)</div>
<div> So my questioin is my way of procedding is wrong or right?</div>
<div> </div>