Thanks for all the help so far.
I tried changing the line for solvopt and bcopt under mm_option.
they now read
"solvopt{Assign}[1-8]" ...
and
"bcopt{Assign}[0156]" ...
instead of
"solvopt{Assign}[1-6]" ...
and
"bcopt{Assign}[156]" ...
I then recompiled and ran MMPBSA.py
Unfortunately, I'm still getting the same error.
Is there another file I need to modify as well?
-Wes
> On Tue, Feb 19, 2013 at 5:34 PM, <wmsmith.uci.edu> wrote:
>
>> 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?
>>
>
> You need to modify the NAB interface as well. At the very least, you have
> to adjust the flex-based input parser to accept the new values. Look in
> $AMBERHOME/AmberTools/src/sff/mm_options.l -- you will have to adjust
> solvopt to accept 8 and bcopt to accept 1's and 0's.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
>
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Received on Tue Feb 19 2013 - 17:00:02 PST
