Jason,
Wes is on the road, so I'll reply on behalf of him ... for his
periodic calculations, he doesn't need any box informations from the
MD trajectories since the PB box is 100% independent of MD box. Also
PBSA only supports rectangular shape right now.
For the tests that Wes is running, it's simply that MMPBSA.py doesn't
allow the new option values for the existing keywords, I think it's
easier to change. We just don't know where these are set in the
script.
However, for Amber13/AmberTool release, end users will need to access
additional keywords in PBSA to use his membrane support, but these are
easier to do down the road.
All the best,
Ray
On Thu, Feb 14, 2013 at 6:45 PM, Jason Swails <jason.swails.gmail.com> wrote:
> I don't know how easy it will be to set up MMPBSA.py to work with periodic
> boundary conditions, since it always strips the box information and solvent.
>
> If it doesn't require box info in the trajectory/topology file, you can use
> -make-mdins to generate the mdin files, modify those variables as needed
> (_MMPBSA_pb.mdin), and then re-run using -use-mdins. If everything works,
> then we can add those variables to the MMPBSA.py input file pretty easily.
> If MMPBSA.py needs substantial changes it may have to wait...
>
> Hope this helps,
> Jason
>
> On Thu, Feb 14, 2013 at 7:01 PM, <wmsmith.uci.edu> wrote:
>
>> Hello everyone,
>> I am working on a modifying the ICCG solver for pbsa to work for
>> periodic boundary conditions. I am at the stage of testing it for use
>> under the MMPBSA to confirm it provides proper results for binding
>> energy calculations.
>> Currently it is bound to solvopt=8 with bcopt=10. Unfortunately, when I
>> put these options into the &pb namelist of my mmbpsa.in file, MMPBSA
>> returns an error of:
>> "Unknown variable bcopt in &pb"
>> I have tracked the message to a line in the "input_parser.py" file for
>> MMPBSA, but I am not sure what needs to be done from here.
>> -Wesley Botello-Smith
>>
>>
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>> AMBER-Developers.ambermd.org
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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Fri Feb 15 2013 - 11:00:03 PST
