Hi,
> 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
[...]
> 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.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 01 2012 - 01:30:03 PDT
