Hi Tsjerk: One of my friends combines popc information into G53a6 that's why i try to use G53a6. If its not working, which force field should i choose?
Best regards, Jenny 2008/11/28 Tsjerk Wassenaar <[EMAIL PROTECTED]> > 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 > -- 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
