On Sun, 6 Aug 2006 14:51:34 -0700 (PDT), Marc Charendoff <[EMAIL PROTECTED]> wrote: > Hey All, > > I'm in the middle of trying to perform a MD sim on a > homoserine lactone. I built the molecule and ran it > through the PRODRG server and retrieved the .gro and > .itp files for processing. I call grompp as such: > > grompp -f minim.mdp -c AHLFIN.GRO -p topol.top -o > input.tpr > > It returns the following: > > Back Off! I just backed up mdout.mdp to > ./#mdout.mdp.1# > checking input for internal consistency... > calling cpp... > processing topology... > Generated 279 of the 1225 non-bonded parameter > combinations > Cleaning up temporary file grompphVMrWO > ------------------------------------------------------- > Program grompp, VERSION 3.3 > Source code file: toputil.c, line: 61 > > Fatal error: > Atomtype 'CS2' not found! > ------------------------------------------------------- What forcefield are you using? For instance, if you use GROMOS96, you have to rename some atomtypes from the gmx gromacs forcefield to the GROMOS, for which CS2 isn't one of the atomtypes. You can figure out how to rename them by comparing the *.atp files for the relevant forcefields (in the top folder). > > > > Last, my topology file looks like the following (and > is borrowed/modified from the methanol tutorial): > > #include "ffG43a1.itp" > #include "AHLGMX.itp" > > [ system ] > AHL > > [ molecules ] > AHL 1 > > I read through Chapter 5, but obviously I'm not > picking up on the nitty gritty details of how to > effectively construct and implement new topologies. > Any guidance would be appreciated. > > Regards, Marc > _______________________________________________ > gmx-users mailing list [email protected] > 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
-- Esther Caballero-Manrique Guenza Group University of Oregon Eugene, OR (USA) _______________________________________________ gmx-users mailing list [email protected] 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
