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

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Wed, 24 Jun 2015 10:06:34 -0700

Norbert,

It's always better to use the latest release to get good support. Note
AmberTools is free and is just updated for this year …

All the best,
Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Wed, Jun 24, 2015 at 8:32 AM, Norbert GARNIER <
norbert.garnier.cnrs-orleans.fr> wrote:
> Dear Jason,
>
> I am using amber11 and a 2.4.3 python version.
>
> Norbert
>
> Le 23/06/2015 14:37, Jason Swails a écrit :
> > On Tue, Jun 23, 2015 at 8:26 AM, Norbert GARNIER <
> > norbert.garnier.cnrs-orleans.fr> wrote:
> >
> >> 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:
> >>
> >> &general
> >>       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,
> >> /
> >> &pb
> >>       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?
> > ​What is nopot?  That doesn't look like any MMPBSA.py variable I'm aware
> > of...  And your strip_mask only strips Na+ and ZNA residues.  Did you not
> > have explicit solvent?
> >
> > Also, what version of AmberTools are you using?
> >
>
> --
> 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 Wed Jun 24 2015 - 10:30:03 PDT