Re: [AMBER] MMPBSA of protein_DNA complex

From: Vlad Cojocaru <>
Date: Tue, 17 Dec 2013 11:49:06 +0100

My advice would be to very carefully test all parameters ... Personally,
I would not rely just on defaults ... Take the MMPBSA manual
and carefully read about each single parameter and try to understand it
.... is a very nice and good attempt to automate the analysis
.. Unfortunately, my feeling is that MMPBSA is not exaclty suitable for
full automation since there are so many approximations that need to be

Linear versus non-linear Poisson Boltzmann is an important issue when
dealing with DNA ... Unfortunately, when you want to do nonlinear PB,
you need to change a number of defaults in a not-exactly straight
forward manner ... You have different alternatives for nonpolar
solvation and quite a number or parameters that one should pay attention
to ... Here only reading the original literature on these models helps
to understand them .. I would argue that the input
is not enough, you need to create your own sander or pbsa input files
.... This is actually a good ideea in any case ...

Please read carefully other papers dealing with MMPBSA on protein/DNA
complexes. but even with these papers out there, I think it would be
good if you choose a test case for which detailed experimental data is
available before you embark yourself in complicated calculations with
predictive goals ..

I hope this helps

On 12/17/2013 11:18 AM, Aditya sarkar wrote:
> Dear all,
> I am new to AMBER molecular dynamics package. I am trying to do MMPBSA
> calculation for a protein-DNA complex. I have gone through the MMPBSA
> tutorial (Using of Ras-Raf complex. Since the tutorial is
> related to protein complex, my question is can I follow the same procedure
> for my protein-DNA complex or not?
> Thanking you in advance
> Aditya
> _______________________________________________
> AMBER mailing list

Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Tue Dec 17 2013 - 03:00:03 PST
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