VMD-L Mailing List

From: Francesco Oteri (francesco.oteri_at_gmail.com)
Date: Sun Dec 12 2010 - 10:00:52 CST

If you need this topology to use vmd for some analisys,
you can obtain in the amber format ( using tleap ) and loading this in vmd

Il 12/12/2010 15:25, leila karami ha scritto:
> 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.
>
> 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?
>
> 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>
> .
> .
> .
> .
> .
> .
> 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?
>
> --
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
>
> Theoretical Physical Chemistry Group
>