Thanks very much!
Anna
-------- Original-Nachricht --------
Datum: Thu, 12 Apr 2007 12:07:08 +0200
Von: Vlad Cojocaru <Vlad.Cojocaru.eml-r.villa-bosch.de>
An: amber.scripps.edu
Betreff: Re: AMBER: topology for postprocessed files?
> 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.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
> >
> >
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
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>
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>
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>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
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Received on Sun Apr 15 2007 - 06:07:18 PDT
