Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex

From: Vlad Cojocaru <>
Date: Tue, 23 Jun 2015 14:53:10 +0200

A change in every single parameter in PBSA can change your dG value quite drastically as well as its sign. We saw quite large differences between sasopt=0 and sasopt=2 and between different values of the internal dielectric constant (see Merino et al Structure 2014). For systems like your I would really advise you to play with the PBSA input directly and use the just as an interface for running the jobs with your predefined inputs.


On June 23, 2015 2:26:07 PM CEST, Norbert GARNIER <> wrote:
>Dear Amber Users
>I have performed 10 ns of MD simulations on a DNA-Protein-Ligand-Na+
>a zinc atom complex with Amber11.
>I would like to calculate the binding free energy of the ligand with
>DNA-Protein part using
>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',
> entropy=1,
> 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 :
>AMBER mailing list

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Received on Tue Jun 23 2015 - 06:00:03 PDT
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