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

From: Vlad Cojocaru <>
Date: Tue, 11 Oct 2016 14:42:25 +0200

Forgot to add that if I change the atom types of parmbsc1 in the
topology as follows: CE->CT, CI->CT, C1->CK, C2->CM, the calculation
proceeds apparently in a correct way ... So, the radii for the ff14SB
atom types seem to be hard coded (I assume as I don't receive any error)
... However, this is definitely not optimal because one does not really
have a control over the use of the radii ... Assigning them in the top
file and using them from there is much better as it gives proper control
over the calculation ...


On 10/11/2016 02:36 PM, 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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