Hi Thomas,
yes there is, check out the ptraj 'center' command, which does exactly
what you describe. Its page 106 of the AT11 manual.
Kind Regards,
Thomas
On Tue, August 3, 2010 7:08 am, Thomas Exner wrote:
> Dear amber users:
>
> I am calculating a protein-ligand complex in explicit water with the
> goal to analyze the first solvents shells. To get all molecules back
> into the original unit cell, I use the image command in ptraj. But since
> the complex is moving in time, it is not in one cell, so that parts of
> the molecule are not surrounded by solvents (I know that there are
> images of the solvents molecules there. But these have to be generated
> by translation of the unit cell, which is not easy to do for an external
> program). Is there a possibility in ptraj or any other program to center
> the unit cell on a specific atom or molecule. Then I could center it on
> the protein and all molecules should then end up in only one cell.
>
> Thank you very much for your help.
> Thomas
>
> --
> ________________________________________________________________________________
>
> Dr. Thomas E. Exner
> Juniorprofessur "Theoretische Chemische Dynamik"
> Fachbereich Chemie
> Universität Konstanz
> 78457 Konstanz
>
> Tel.: +49-(0)7531-882015
> Fax: +49-(0)7531-883587
> Email: thomas.exner.uni-konstanz.de
> ________________________________________________________________________________
>
>
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>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Aug 03 2010 - 04:30:05 PDT
