<div>Hi all:</div>
<div>I have a problem with grompp</div>
<div>I want to making "POPC+protein" file</div>
<div>and I search the archieve and follow the process</div>
<div>1.run pdb2gmx for protein only</div>
<div>2.add below parameters into my topology file</div>
<div> #include "ffG53a6.itp"<br> #include "lipid.itp"<br> #include "popc.itp"<br>3.adjust the [ molecules ] section to list the number and type of my components <br clear="all">4.run editconf and genbox<br>
5.run grompp and it shows</div>
<div>Fatal error:<br>Atomtype CA not found</div>
<div> </div>
<div><strong>Below is all information it shows</strong></div>
<div><strong>Can someone help me to solve this problem?</strong></div>
<div><strong>I am appreciate with that.</strong></div>
<div><strong>Thaks.</strong></div>
<div> :-) G R O M A C S (-:<br> Getting the Right Output Means no Artefacts in Calculating Stuff<br> :-) VERSION 4.0 (-:<br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, <span class="t_tag" onclick="tagshow(event)" href="tag.php?name=The">The</span> Netherlands.<br> Copyright (c) 2001-2008, The GROMACS development team,<br>
check out <a href="http://www.gromacs.org/" target="_blank">http://www.<span class="t_tag" onclick="tagshow(event)" href="tag.php?name=gromacs">gromacs</span>.org</a> for more information.<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> :-) grompp (-:<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 1UEO-nowater_water.gro Input Structure file: gro g96 pdb tpr tpb<br> 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 1UEO-nowater.top Input Topology file<br>-pp processed.top Output, Opt. Topology file<br> -o 1UEO-nowater_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>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>Ignoring obsolete mdp entry 'title'<br>
Ignoring obsolete mdp entry 'cpp'<br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#<br>checking input for internal consistency...<br>processing topology...<br>Opening library file /usr/local/md/share/gromacs/top/ffG53a6.itp<br>
Opening library file /usr/local/md/share/gromacs/top/ffG53a6nb.itp<br>Opening library file /usr/local/md/share/gromacs/top/ffG53a6bon.itp<br>Opening library file /usr/local/md/share/gromacs/top/ff_dum.itp<br>WARNING 1 [file lipid.itp, line 14]:<br>
Overriding atomtype LO<br>WARNING 2 [file lipid.itp, line 15]:<br> Overriding atomtype LOM<br>WARNING 3 [file lipid.itp, line 16]:<br> Overriding atomtype LNL<br>WARNING 4 [file lipid.itp, line 17]:<br> Overriding atomtype LC<br>
WARNING 5 [file lipid.itp, line 18]:<br> Overriding atomtype LH1<br>WARNING 6 [file lipid.itp, line 19]:<br> Overriding atomtype LH2<br>WARNING 7 [file lipid.itp, line 20]:<br> Overriding atomtype LP<br>WARNING 8 [file lipid.itp, line 21]:<br>
Overriding atomtype LOS<br>WARNING 9 [file lipid.itp, line 22]:<br> Overriding atomtype LP2<br>WARNING 10 [file lipid.itp, line 23]:<br> Overriding atomtype LP3<br>WARNING 11 [file lipid.itp, line 24]:<br> Overriding atomtype LC3<br>
WARNING 12 [file lipid.itp, line 25]:<br> Overriding atomtype LC2<br>WARNING 13 [file lipid.itp, line 108]:<br> Overriding non-bonded parameters,<br> old: 0.00238804 3.38411e-06 new<br>LNL C 1 2.387718e-03 2.389594e-06<br>
-------------------------------------------------------<br>Program grompp, VERSION 4.0<br>Source code file: toppush.c, line: 793<br>Fatal error:<br>Atomtype CA not found</div>
<div> </div>
<div> </div>
<div>-- <br>Jenny Hsu, Biotechnology Dept., <br>Ming Chuan University, Taiwan, R.O.C<br></div>