VMD-L Mailing List

From: leila karami (karami.leila1_at_gmail.com)
Date: Sun Dec 12 2010 - 08:25:03 CST

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