<div>Hi Tsjerk:</div>
<div> </div>
<div>One of my friends combines popc information into G53a6</div>
<div>that's why i try to use G53a6.</div>
<div>If its not working, which force field should i choose?</div>
<div> </div>
<div>Best regards,</div>
<div>Jenny<br><br></div>
<div class="gmail_quote">2008/11/28 Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Jenny,<br><br>The files lipid.itp/popc.itp contain references to atom types which<br>are not in the G53a6 force field; that combination just doesn't work.<br>
lipid.itp/popc.itp were written to be used with another force field.<br>It's generally not a good idea to mix force fields.<br><br>Cheers,<br><br>Tsjerk<br>
<div>
<div></div>
<div class="Wj3C7c"><br>On Fri, Nov 28, 2008 at 8:58 AM, Jenny Hsu <<a href="mailto:jenny.h1087@gmail.com">jenny.h1087@gmail.com</a>> wrote:<br>> Hi all:<br>> I have a problem with grompp<br>> I want to making "POPC+protein" file<br>
> and I search the archieve and follow the process<br>> 1.run pdb2gmx for protein only<br>> 2.add below parameters into my topology file<br>> #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<br>> components<br>> 4.run editconf and genbox<br>> 5.run grompp and it shows<br>> Fatal error:<br>
> Atomtype CA not found<br>><br>> Below is all information it shows<br>> Can someone help me to solve this problem?<br>> I am appreciate with that.<br>> Thaks.<br>> :-) 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, The Netherlands.<br>> Copyright (c) 2001-2008, The GROMACS development team,<br>> check out <a href="http://www.gromacs.org/" target="_blank">http://www.gromacs.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<br>
> 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<br>> 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<br>><br>><br>> --<br>
> Jenny Hsu, Biotechnology Dept.,<br>> Ming Chuan University, Taiwan, R.O.C<br>><br></div></div>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br><br><br><br>--<br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623<br>
_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Jenny Hsu, Biotechnology Dept., <br>
Ming Chuan University, Taiwan, R.O.C<br>