VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri May 30 2008 - 05:20:24 CDT

Hi Matthieu,

You might find pbctools very useful for that purpose:

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

Use the "pbc unwrap" command to unwrap the coordinates of the complex.

Hope it helps,

Cheers,
Michel

On Fri, May 30, 2008 at 11:12 AM, Matthieu Chavent
<matthieu.chavent_at_edam.uhp-nancy.fr> wrote:
> Hello All,
>
> I have a problem: I created a water box around a protein complex to perform
> MD simulations. During the MD a protein moved out the water box and was
> placed at the opposite side of the water box (thank to periodic conditions).
> I would like to save the trajectory in a pdb file, but when I use save
> coordinates the positions of the two proteins are saved at each side of the
> water box and I can't analyze the results (calculate RMSD, residues in
> contact, etc..). I think that It is possible to move one of the two protein
> to reconstruct the complex.. But I don't know how..
>
> Could you help me please...
>
> Thank you in advance!
>
> Matthieu Chavent (PhD student)
>