VMD-L Mailing List

From: Diego Enry (diego.enry_at_gmail.com)
Date: Thu Apr 28 2011 - 10:20:02 CDT

Hey, you may find these very usefull

http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/node6.html

http://dogmans.umaryland.edu/~kenno/tutorial/

Also there's also some great material here:
http://mmtsb.org/workshops/mmtsb-ctbp_2006/mmtsb-ctbp_2006.html

In this las link, look for this PDF
CHARMM force fields, parameterization strategies and future/ongoing force
field developments. (MacKerell) (download
lecture)<http://mmtsb.org/workshops/mmtsb-ctbp_2006/Lecture_pdf/params_alex_jul06a.pdf>

On Thu, Apr 28, 2011 at 3:24 PM, Markus K. Dahlgren <
markus.dahlgren_at_yale.edu> 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 <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
>> *
>>
>>
>
> 

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