Hello Thomas and Aldo
Thanks for your advices, I have just solved the problem by choosing as
complex the system on which I wanted to perform the calculation. For
example, although my complex is a dimer with two ligands, I only took
into account the first monomer with its ligand to run the
extract_coords.mmpbsa script and then binding_energy.mmpbsa.
Best regards
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 the
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?
You need to be more precise about what you actually want to calculate.
The
binding free energy of two ligands can be computed in MMPBSA by setting
both of them as LIGAND and the rest of the system (a protein with two
binding sites I guess?) as RECEPTOR. You would not need to make changes
in
the code for that, I assume.
Alternatively, you could compute the binding energy of either ligand in
the presence or absence of the other one (Removing the second one or
including it with RECEPTOR). Cooperativity between the ligands will
make
the sum of both binding energies different from the binding energy of
both
of them.
Hello Thomas
-------- Original Message --------
Subject: Re: [AMBER] Trouble calculating free energy
Date: Fri, 1 Jun 2012 22:48:34 -0700 (PDT)
From: Aldo Segura <asegurac666.yahoo.com.mx>
To: AMBER Mailing List <amber.ambermd.org>
Reply-To: AMBER Mailing List <amber.ambermd.org>
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
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Received on Sat Jun 02 2012 - 07:00:02 PDT
