From: Matthieu Chavent (matthieu.chavent_at_edam.uhp-nancy.fr)
Date: Fri May 30 2008 - 10:40:00 CDT

Thank you very much Michel!!

   You give me the good direction: I resolved my problem with the pbc
join function.. I have just a remark on it: when I loaded the VMD 1.8.6
package there is the PBCtools 2.0 package but not the PBCtools 2.1.. I
think that this new version gives very useful new functions (as join
function ;o) ), so that you could add it in the current version of VMD
(if it has not already done..)

   I would like to thank the developers of this tool.

    Matthieu

L. Michel Espinoza-Fonseca a écrit :
> 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)
>>
>>
>
>