Hi Jenny, The files lipid.itp/popc.itp contain references to atom types which are not in the G53a6 force field; that combination just doesn't work. lipid.itp/popc.itp were written to be used with another force field. It's generally not a good idea to mix force fields.
Cheers, Tsjerk On Fri, Nov 28, 2008 at 8:58 AM, Jenny Hsu <[EMAIL PROTECTED]> wrote: > Hi all: > I have a problem with grompp > I want to making "POPC+protein" file > and I search the archieve and follow the process > 1.run pdb2gmx for protein only > 2.add below parameters into my topology file > #include "ffG53a6.itp" > #include "lipid.itp" > #include "popc.itp" > 3.adjust the [ molecules ] section to list the number and type of my > components > 4.run editconf and genbox > 5.run grompp and it shows > Fatal error: > Atomtype CA not found > > Below is all information it shows > Can someone help me to solve this problem? > I am appreciate with that. > Thaks. > :-) G R O M A C S (-: > Getting the Right Output Means no Artefacts in Calculating Stuff > :-) VERSION 4.0 (-: > Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2008, The GROMACS development team, > check out http://www.gromacs.org for more information. > This program is free software; you can redistribute it and/or > modify it under the terms of the GNU General Public License > as published by the Free Software Foundation; either version 2 > of the License, or (at your option) any later version. > :-) grompp (-: > Option Filename Type Description > ------------------------------------------------------------ > -f em.mdp Input, Opt! grompp input file with MD parameters > -po mdout.mdp Output grompp input file with MD parameters > -c 1UEO-nowater_water.gro Input Structure file: gro g96 pdb tpr > tpb > tpa > -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa > -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa > -n index.ndx Input, Opt. Index file > -p 1UEO-nowater.top Input Topology file > -pp processed.top Output, Opt. Topology file > -o 1UEO-nowater_em.tpr Output Run input file: tpr tpb tpa > -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt > -e ener.edr Input, Opt. Energy file: edr ene > Option Type Value Description > ------------------------------------------------------ > -[no]h bool no Print help info and quit > -nice int 0 Set the nicelevel > -[no]v bool yes Be loud and noisy > -time real -1 Take frame at or first after this time. > -[no]rmvsbds bool yes Remove constant bonded interactions with virtual > sites > -maxwarn int 0 Number of allowed warnings during input > processing > -[no]zero bool no Set parameters for bonded interactions without > defaults to zero instead of generating an error > -[no]renum bool yes Renumber atomtypes and minimize number of > atomtypes > Ignoring obsolete mdp entry 'title' > Ignoring obsolete mdp entry 'cpp' > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# > checking input for internal consistency... > processing topology... > Opening library file /usr/local/md/share/gromacs/top/ffG53a6.itp > Opening library file /usr/local/md/share/gromacs/top/ffG53a6nb.itp > Opening library file /usr/local/md/share/gromacs/top/ffG53a6bon.itp > Opening library file /usr/local/md/share/gromacs/top/ff_dum.itp > WARNING 1 [file lipid.itp, line 14]: > Overriding atomtype LO > WARNING 2 [file lipid.itp, line 15]: > Overriding atomtype LOM > WARNING 3 [file lipid.itp, line 16]: > Overriding atomtype LNL > WARNING 4 [file lipid.itp, line 17]: > Overriding atomtype LC > WARNING 5 [file lipid.itp, line 18]: > Overriding atomtype LH1 > WARNING 6 [file lipid.itp, line 19]: > Overriding atomtype LH2 > WARNING 7 [file lipid.itp, line 20]: > Overriding atomtype LP > WARNING 8 [file lipid.itp, line 21]: > Overriding atomtype LOS > WARNING 9 [file lipid.itp, line 22]: > Overriding atomtype LP2 > WARNING 10 [file lipid.itp, line 23]: > Overriding atomtype LP3 > WARNING 11 [file lipid.itp, line 24]: > Overriding atomtype LC3 > WARNING 12 [file lipid.itp, line 25]: > Overriding atomtype LC2 > WARNING 13 [file lipid.itp, line 108]: > Overriding non-bonded parameters, > old: 0.00238804 3.38411e-06 new > LNL C 1 2.387718e-03 2.389594e-06 > ------------------------------------------------------- > Program grompp, VERSION 4.0 > Source code file: toppush.c, line: 793 > Fatal error: > Atomtype CA not found > > > -- > Jenny Hsu, Biotechnology Dept., > Ming Chuan University, Taiwan, R.O.C > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
