You could decompose the ligand into covalently connected fragments or residues ... similar to the treatment of a protein.
++++++++++++++++++++++++++++++++++++++++++++++++++
Alexander Metz (PhD Student)
Heinrich Heine Universität Düsseldorf
Institut für Pharmazeutische und Medizinische Chemie
Computational Pharmaceutical Chemistry
Universitaetsstrasse 1
40225 Düsseldorf, Germany
Tel: +49 211 81 13854
++++++++++++++++++++++++++++++++++++++++++++++++++
________________________________
Von: Jason Swails <jason.swails.gmail.com>
An: AMBER Mailing List <amber.ambermd.org>
Gesendet: 12:11 Donnerstag, 20.Juni 2013
Betreff: Re: [AMBER] Is per atome decomposition in MM-PBSA possible?
On Thu, Jun 20, 2013 at 5:37 AM, Haralambos Tzoupis <tzoupis.eie.gr> wrote:
> Dear Amber users,
>
>
>
> I have been using MM-PBSA (AMBER 11) for free energy calculations of a
> protease-ligand complex. According to manual, there is the possibility of
> per residue and pair wise decomposition of binding energy.
>
>
>
> Is it possible to perform per atom decomposition for a ligand/drug, namely
> to see the energy contributions for individual ligand atoms (C, N, O etc.)?
>
No it's not currently possible.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 20 2013 - 04:00:02 PDT
