VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Dec 13 2010 - 04:03:50 CST

dear leila,

On Sun, Dec 12, 2010 at 9:25 AM, leila karami <karami.leila1_at_gmail.com> wrote:
> Dear VMD users
>
> I did simulation of protein-dna complex in water solvent by amber03
> forcefield in gromacs package.
>
> I need to psf file. I use automatic PSF builder in vmd for making psf file.

you are very optimistic. the automatic psf builder is
meant for creating .psf files for routine tasks and requires
well behaved .pdb files.

> I have some questions:
>
> 1) in step 1 in topology files section,
>
> Should I chose a particular topology? or Should the default value is
> selected?

you need a topology file that matches your system.
the word topology file may be a little misleading,
'topology and residue template file' might be more
correct. if you want to use the psf file for a simulation,
then it has to match the parameter file that you want
to use later.

>
> I selected default value.
>
> 2) my pdb file contains protein, DNA, Na+ and water. in step 2, I selected
> everything.
>
> 3) in step 3, when select create chains, first in vmd console I encountered
>
> warning : I found some undefined atom types in <SOL>

it seems that your .pdb file does not follow the expected
naming conventions from the topology file. you have to fix
this in the pdb file or use psfgen manually (instead of the
autopsf frontend). there you have more detailed options
to adjust the psfgen settings to your input.

> then wmd is closed automatically.
>
> water solvent in my pdb file is marked by SOL.
>
> I didn't use step 4.
>
> is my manner in 3 steps true?

probably not.

axel

> --
>
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
>
> Theoretical Physical Chemistry Group
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.