I have tried using the -make-mdins and -use-mdins options with MMPBSA.py .
As suggested, I generated the .mdin files using -make-mdins. I then modify
the values for the bcopt and solvopt flags under the .mdin file generated
for the pb run as needed. Then I ran MMPBSA.py again using -use-mdins.
As expected, the gb ran normally.
Unfortunately, when the program hits the pb run a new (but very similar)
error message appears:
"Error: mm_option: unknown keyword or invalued value: solvopt"
It looks like there is another check or something that is blocking use of
the solvopt and bcopt values needed.
Do you have any idea what I would need to change so I can get it to run?
-Wes
> 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
>>>
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Tue Feb 19 2013 - 15:00:03 PST
