VMD-L Mailing List

From: Yu Fang (y.fang2_at_ugrad.unimelb.edu.au)
Date: Wed Dec 09 2009 - 22:17:57 CST

Hi All

I have a question regarding the vmd paratool plugin
As I understand it this plugin is capable of reading the gaussian QM
simluation log files and computing the CHARMM force field parameters for
bonds, angles and dihedrals based on this information.

I understand how the CHARMM topology & parameter files work for NAMD, but
I am new to gaussian. I am trying to parametize a few small ligand
molecules, for which comparison to atom types in the default parameter
file that comes with namd is not good enough.

What I have done is
-selected atom types and assigned VDW parameters (using default
topology/parameter file that comes with namd)
-autogenerated internal co-ordinates
-performed the optimized geometry and single point calcs in gaussian as
required by paratool and imported in the respective log files
successfully.

However, I cannot figure out what to do next to get paratools to generate
the CHARMM parameters for me.

I tried to perform a co-ordinate transformation QM job in gaussian,
thinking this might be required. As I said, I am new to gaussian, so I do
not know what this job does. Anyhow the gaussian input file paratool
generated for me did not work, I suspect because I am using g98 instead of
g03.

This gaussian input file options are shown below:

%chk=dopamine_transf.chk
%nproc=1
%mem=1GB
# RHF/6-31G* Geom=(AllCheck,ModRedundant) Freq=(Modredundant,ReadFC)
IOp(7/33=2)
(numbers follow)

running this file, g98 seems to complain that "Freq=(Modredundant,ReadFC)"
contained a syntax error.

The gaussian log file looks like the following:

 *********************************************
 Gaussian 98: x86-Linux-G98RevA.7 11-Apr-1999
                  10-Dec-2009
 *********************************************
 %chk=dopamine_transf.chk
 %nproc=1
 Will use up to 1 processors via shared memory.
 %mem=1GB
 Default route: MaxDisk=2000MW
 ----------------------------------------------------------------------
 # RHF/6-31G* Geom=(AllCheck,ModRedundant) Freq=(Modredundant,ReadFC) I
 Op(7/33=2)
 ----------------------------------------------------------------------
  QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.
 MODREDUNDANT) FREQ=(MODREDUNDANT,READFC)

So, in short, I would like to know what I need to do next to generate the
CHARMM parameters using paratools. If I need to perform a co-ordinate
transformation gaussian job, what are the options I should use in the
input file for g98.

Any help much appreciated.
Yu