Dir Tom, I have a version of ffG53a6.rtp with PTR. It worked for me in simulations, though I never rigorously checked the FF parameters, so no warranty. Contact me off list if you're interested.
Ran. Tom Lenaerts wrote: > Hi all, > > > To work with PTR in gromacs I added the residue information in > ffG53a6.rtp, added the unknown atom names () to ffG53a6.atp and added > the residue name to aminoacids.dat. > this allowed me to make the topology file using pdb2gmx, create the > box and fill it with water. Now I want to perform the > energy minimisation by first doing grompp. Then > I get an error > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# > checking input for internal consistency... > calling /usr/bin/cpp... > processing topology... > Generated 165 of the 1596 non-bonded parameter combinations > Cleaning up temporary file grompp8BMpzT > ------------------------------------------------------- > Program grompp, VERSION 3.3 > Source code file: toputil.c, line: 61 > > Fatal error: > Atomtype 'CB' not found! > ------------------------------------------------------- > > > Yet I added the atom CB to the ffG53a6.atp file ... so what can be the > problem here? > > Tom > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------
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