Hello!
You should try to use the python version of MMPBSA. Then, you can check in the manual the "mask" option to define each element of the complex.
Saludos!
=======================================
Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegurac.ipn.mx; aldosegura.gmail.com
=========================================
--- El jue 31-may-12, bmartini <bmartini.ibt.unam.mx> escribió:
De: bmartini <bmartini.ibt.unam.mx>
Asunto: [AMBER] Trouble calculating free energy
A: "Amber" <amber.ambermd.org>
Fecha: jueves, 31 de mayo de 2012, 22:14
Hello everyone
I have experienced some troubles calculating the free energy between a
protein with two receptors and two ligands, each one bounded to its
respective receptor. I have followed a tutorial in which the free energy
is performed using mm_pbsa.pl on amber´s web site, but they are intended
to deal with systems where you have a receptor and a ligand. I
understand that some changes have to be done in extract_coords.mmpbsa
and binding_energy.mmpbsa in order to get the separated energy
contribution for each receptor and its ligand. Could anyone give me a
hand?
Thanks in advance
Thanks in advance
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Received on Fri Jun 01 2012 - 23:00:02 PDT
