Re: AMBER: topology for postprocessed files?

From: Vlad Cojocaru <>
Date: Thu, 12 Apr 2007 12:07:08 +0200

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 ..

vlad 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,

Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
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Received on Sun Apr 15 2007 - 06:07:17 PDT
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