AMBER Archive (2007)

Subject: Re: AMBER: topology for postprocessed files?

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Apr 12 2007 - 05:07:08 CDT

Dear Anna,

You can create a pdb file with your stripped system and reload it into
Leap and save the new topology file ...\
As for the energies, you can do a single step calculation with sander on
the snapshot(s) that you are interested in ..

Best
vlad

anna.schrey_at_gmx.de wrote:

>Deas Amber community,
>
>I would like to postprocess trajectories that way that I have to remove cetrain residues (e.g. a ligand) and calculate the energies afterwerds. The trajecotries are no problem, they can be modified that way using ptraj. But how to get the corresponding topology file? And how can I calculate the energies (e.g. E_el and E_vdw) with SANDER?
>
>kind regards,
>
>Anna
>
> 

-- 
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Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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