Hi Vlad,
The radii are hardcoded in $AMBERHOME/AmberTools/src/pbsa/sa_driver.F90
(see "subroutine pb_aaradi"). Unfortunately this implementation leads to
the "missing radii" problems you encountered because the PBSA developers
and force field developers aren't always in communication when new atom
types are added.
For a short term fix, you can add the new atom types by analogy to
sa_driver.F90 yourself and recompile. But reporting here is a good idea
too so that developer's can make updates.
--Niel
On Tue, Oct 11, 2016 at 6:12 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Hi Carlos,
>
> Thanks for your thoughts ....
>
> PBSA is the actual program that does the PB calculations and its also
> incorporated into Sander (which is then used by MMPBSA.py)... Its
> options are provided in the &cntrl and &pb namelists.
>
> When using radiopt=1 option for PB calculations, the radii used are not
> those from the topology file, but rather a set that is optimized for
> Amber atom types based on Tan & Luo J.Phys.Chem 2006 and is hard coded
> into PBSA (Sander)....
>
> So, my question was whether this set is continuously updated with the
> new atom types in newer force fields ... If not, is there a way to
> assign this set in the topology and then use radiopt=0 (read radii from
> topology) ?
>
> Sure, I could start testing the effect of the radii but no way I could
> put this high on priority list at present ... We have previously used
> the default hard-coded set with good results ...
>
> Best
> Vlad
>
> On 10/11/2016 02:57 PM, Carlos Simmerling wrote:
> > 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 mmpbsa.py 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 <
> > vlad.cojocaru.mpi-muenster.mpg.de> 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]mpi-muenster.mpg.de
> >> http://www.mpi-muenster.mpg.de/43241/cojocaru
> >>
> >>
> >> _______________________________________________
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> >>
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>
> --
> 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
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
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Received on Tue Oct 11 2016 - 07:30:02 PDT
