VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Dec 25 2010 - 11:20:06 CST

On Sat, Dec 25, 2010 at 10:14 AM, leila karami <karami.leila1_at_gmail.com> wrote:
> Dear VMD users
>
> happy christmas
>
> I did simulation of protein-dna complex in water solvent (TIP3P). I
> converted gromacs trajectory file (xtc) to amber trajectory
> file (mdcrd) by VMD. when I see converted mdcrd file by vmd, protein and dna
> are normal but there is a problem about
> water molecules: 1) the length of O-H bonds are longer than those of normal
> waters. 2) there are new bonds between H atoms
> of each water molecule.

both the xtc and the mdcrd format only contain coordinate
information, but no information about atom types and so on,
so VMD can only show you bonds and atom types/names
from a topology file that you load first.

if that topology file and the actual atom identities don't match,
then you get all kinds of funny things.

> is this state normal? is it a visual program? Do trajectory file conversion
> done correctly?

VMD does what you tell it to do and you see what you give it
to read. you have to know by yourself, whether you are loading
the correct groups of files.

> how to fix it?

how should anybody know?

axel.

> any help will highly appreciated
>
>
>
> --
>
> 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.