VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 19 2009 - 08:51:46 CDT

On Mon, 2009-10-19 at 11:21 +0300, Stanislaw Bobritsky wrote:
> Hi, everyone!
>
> I work with membrane which contains POPS and cholesterol. Hence I have
> to parametrize these molecules.
>
> I have successfully defined atom types, bond orders, etc, but I have a
> trouble with optimized geometry, because optimization was performed
> with GAMESS, which results not supported output. Thus I have following
> error message: "Couldn't read 'Input orientation'".
>
> I tried to convert GAMESS to GAUSSIAN output with Babel, but the error
> remains the same.

have you looked at what babel does to files?
and where does it support gaussian _output_??

quantum chemistry codes have so many ad-hoc formatted outputs that it
is basically impossible to emulate the output from one code based on
the output of another, especially, when you care about more than just
the basics like coordinates.

> How can I fix it to obtain correct parameter files?

did you have a look at the CHARMM force field home page?

check out:
http://mackerell.umaryland.edu/CHARMM_ff_params.html
and:
http://mackerell.umaryland.edu/Empirical_FF_Dev.html

there are many references and comments on how to parametrize
molecules and notes on how to get parameters for specific
types of molecules.

cheers,
   axel.

> *sorry if this question was already asked here, but I didn't find it
> =(
>
> Stanislaw Bobritsky,
> ChemBio Center, Taras Shevchenko National University,
> Kiev, Ukraine 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.