AMBER Archive (2006)

Subject: AMBER: About mm_pbsa calculation setting up

From: alfredoq_at_fcq.unc.edu.ar
Date: Thu May 11 2006 - 21:19:03 CDT

Dear Amber Community: I have one question regarding the setting up of the
mm_pbsa.in file in order to calculate the binding free energy from a
trajectory. I have read that the mm_pbsa analisys is performed to a molecular
dynamic run in which the solvent is explicitly present. Also that the water
molecules (and also ions) should be stripped out to perform this analysis. I
found in the mm_pbsa.in file in the examples that in order to calculate the
binding energy the prmtop files should be indicated. Here is that my first
question arises: should be these prmtop files belong to the whole system, that
is the file containing waters and ions?. If this is affirmative, do I need to
create the prmtop files for the ligand and the macromolecule in the same
conditions?
Thanks in advance for the hints,
All the best

Alfredo Quevedo
Facultad de Ciencias Químicas
Universidad Nacional de Córdoba

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