From: Diego Enry (
Date: Thu Apr 28 2011 - 10:20:02 CDT

Hey, you may find these very usefull

Also there's also some great material here:

In this las link, look for this PDF
CHARMM force fields, parameterization strategies and future/ongoing force
field developments. (MacKerell) (download

On Thu, Apr 28, 2011 at 3:24 PM, Markus K. Dahlgren <> wrote:

> 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 <>:
> 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
>> *

Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.