[AMBER] MMGBSA, Generalized Born, protein-nucleic acid complex

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Thu, 24 Oct 2013 14:53:45 +0200

Dear all,

We are attempting some MMGBSA calculations on a protein-nucleic acid
complex and we'd like to get some feed-back on the generalized born
For the record, we are using ff99SB/ildn/nmr force field variant.

I know that generally igb=1 has been tested and recommended on nucleic
acids. According to the original work by Vickei Tsui and Dave Case,
igb=1 + mbondi radii with the parameter changes highlighted in the
AmberTools manual is the preferred combination for nucleic acids.

I also know that for proteins igb=5 and the new igb=7 and igb=8 +
mbondi2 are performing better.

My question is: what about state-of-the-art for protein-nucleic acid
complexes ? Is anybody willing to share some latest experiences and some
new relevant references about the choice of parameters ?

Thanks for any insights,

Best wishes

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]mpi-muenster.mpg.de
AMBER mailing list
Received on Thu Oct 24 2013 - 06:00:03 PDT
Custom Search