[AMBER] MMPBSA on DNA-Protein-Ligand complex

From: Norbert GARNIER <norbert.garnier.cnrs-orleans.fr>
Date: Tue, 23 Jun 2015 14:26:07 +0200

Dear Amber Users

I have performed 10 ns of MD simulations on a DNA-Protein-Ligand-Na+ and
a zinc atom complex with Amber11.
I would like to calculate the binding free energy of the ligand with the
DNA-Protein part using MMPBSA.py.

My input file is the following:

     startframe=1, interval=5, endframe=5000, keep_files=2
     receptor_mask=':1-299', ligand_mask=':300',
     strip_mdcrd=1, strip_mask=':Na+:ZNA',
     nopot=1, cavity_surften=0.0378, cavity_offset=-0.5692,
     fillratio=4, scale=2.0,
     linit=1000, prbrad=1.4, radiopt=0,
Is this input file is correct?

With this input file I obtain positive DELTA G binding value.

Could you please give me some advices?
Thank you very much.


Dr. Norbert GARNIER
Assistant Professor of physics - Orléans University
« DNA repair: structural and functional approaches»
Centre de Biophysique Moléculaire, UPR4301, CNRS
Rue Charles Sadron
CS 80054
45071 Orléans cedex 2
Tel: +33 (0)2 38 25 76 68
Web site : http://cbm.cnrs-orleans.fr/
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Received on Tue Jun 23 2015 - 05:30:04 PDT
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