Hi,
I guess there is some misunderstanding in terminology:
Altough you may specify several ligand or receptor groups within the
input for mm_pbsa.pl, all groups are united to represent one ligand and
one receptor during computation.
So, if you want to computed the interaction energy of all 6 ligands with
all 11 chains in total, you list all ligand atoms as LIG groups and all
receptor atoms als REC groups. Internally, theese groups are then taken
together.
The mm_pbsa.pl script does not compute the interaction energies between
several LIG and REC groups atomatically! The GROUP notation is just to
allow the user to specify atoms that do not come linearily in the atom list.
From your given definition of ligand and receptor groups I think, that
you misunderstood the meaning of the variables.
In your input case, there is one REC group (atom 1-4584) and one LIG
group (atom 4585-5034).
If you intend to compute interaction energies between certain ligands
and receptor chains, you have to extract these substructures from your
snapshots. Note, however, that the topology file must correspond to the
extracted coordinate file.
Regards,
Anselm
Bioinformatik
Institut für Biochemie
Friedrich-Alexander-Universität Erlangen-Nürnberg
Germany
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Received on Tue Jul 31 2012 - 05:00:03 PDT
