[gmx-users] Attempting small molecule . . .

Marc Charendoff mcharend at sbcglobal.net
Sun Aug 6 23:51:34 CEST 2006

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

It returns the following:

Back Off! I just backed up mdout.mdp to
checking input for internal consistency...
calling cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter
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 ]

[ molecules ]

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 

More information about the gromacs.org_gmx-users mailing list