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

From: Carlos Simmerling <>
Date: Tue, 11 Oct 2016 08:57:04 -0400

I'm not sure what you mean by hard coded. If you set radii in Leap, they
are not hard coded. Or is it in the script that you mean? Just
not sure which program is "PBSA".

Our recent changes to radii are based on comparing GB to explicit water,
but the GB is already fit to PB so in principle it doesn't matter which
implicit solvent is used. Of course it might matter, so you can look into
recent studies where different radii sets are optimized for the type of
work you're doing. Unfortunately I've seen ones for small molecule binding
or for solvation energies, but I have not seen any studies examining the
effect of radii on protein-DNA complexes. You might need to try some
options yourself.

On Tue, Oct 11, 2016 at 8:36 AM, Vlad Cojocaru <> wrote:

> 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
> Vlad
> --
> 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]
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Received on Tue Oct 11 2016 - 06:00:04 PDT
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