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! ------------------------------------------------------- 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 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