VMD-L Mailing List

From: Markus K. Dahlgren (markus.dahlgren_at_yale.edu)
Date: Thu Apr 28 2011 - 08:24:52 CDT

Hi Shome,

You need to create a topology file of the ligand that has the following parts:
MASS of all atomtypes
Atom names, atomtypes, atomic partial charges and total residue charge.
All bonds,
All impropers

Then you need to match the atom names in the topology to the atomnames in your
pdb file.

Finally you need to append all parameters that belong to your ligand to the
parameter file. These parameters you find in any force field parameter list
(CHARMM, OPLSAA, AMBER, etc). You need to use the same forcefield for your
protein, ligand and solvent.

The topology file is described in detail in the NAMD tutorial. Once you
have the
topology you can create a psf file of the complex.

Good luck!
Markus

Quoting shome sankar bhunia <shome.sankar_at_gmail.com>:

> DEAR VMD users
>
> I want to run a Molecular dynamics simulation of a ligand protein complexin
> VMD for which i have to parametrize my ligand. For that i have installed
> GAMESS on my linux ubuntu10.10.
> my question is how to parametrize the ligand using GAMESS. i just want to
> know the basic steps *,* as I know first of all i have to do geometry
> optimization, than what are the steps i have to perform. i do not need any
> scripts that i will try to find myself and next ... what output of GAMESS
> may be a input for VMD? i mean to say the file extension ..... actually i am
> getting a *.dat* file after the GAMESS run.
>
> thanks in advance
>
>
> --
>
> *Regards
> **Shome Sankar Bhunia
> Medicinal & Process Chemistry Division
> Central Drug Research Institute
> India
> *
>