[gmx-users] Attempting small molecule . . .

[Marc Charendoff]

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