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 - 06:30:03 PDT
