[AMBER] mmpbsa with atomic radii for ff14SB and parmbsc1 atom types

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Tue, 11 Oct 2016 14:36:50 +0200

Dear all,

I am trying to reproduce some of our previous MMPBSA results on
protein-DNA complexes using ff14SB and parmbsc1 force fields (using
sander) ...
When running PBSA with radiopt=1, I got complaints about missing radii
for the atomtypes of parmbsc1 ...

Could somebody tell me based on which force field combination (protein,
nucleic acids) are the atomic radii hard coded in sander for PB
calculations derived ? Are the atoms types of ff14SB included ?

Is there a way to not rely on those hard-coded optimized radii and
assign them in the topology file and then use radiopt=0 ? As far as I
know the radii sets available in Leap (mbondi, mbondi2, mbondi3 are
optimized for GB and not PB. Am I right here or can these be used for
PB as well ?

Thanks for any advice on this

Best wishes

Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Tue Oct 11 2016 - 06:00:03 PDT
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