AH! That did it. I tried again with a clean clone of the pbsa-dev branch
and everything works (after the modifications discussed). It looks like my
version was missing a couple of patches.
Thanks again for being patient.
-Wes
> Is this code visible to us? pbsa-dev branch? master branch?
>
> My guess is that somehow you're using an old nab without the changes to
> build mmpbsa_energy.nab. Maybe you're using the nab from another
> installation? Are you sure that you're rebuilding nab in serial after
> your
> changes? (Note, it's not enough to just rebuild MMPBSA.py -- you also
> have
> to rebuild NAB). I've changed the mm_options.l file a few times before
> (added some values for e_debug and gb), and it's always worked like I
> expected.
>
> So _something_ must be happening that you/we are not aware of to be
> causing
> this behavior.
>
> I would suggest writing your own separate nab program that just calls
> mm_options() with the 'new' parameters (and maybe mm_init just so they get
> 'used') and debugging with that until this issue is resolved. (You can
> basically take the code from mmpbsa_energy.nab and cut out the fluff).
>
> HTH,
> Jason
>
> On Fri, Feb 22, 2013 at 4:07 PM, <wmsmith.uci.edu> wrote:
>
>> Using the fprintf line just before the mm_options call, I get back:
>>
>> "solvopt=8, accept=0.001000, maxitn=1000, fillratio=4.000000,
>> space=0.50000"
>>
>> ... although now i'm getting the
>>
>> "mm_option: unknown keyword or invalid value: solvopt"
>>
>> Error once again.
>>
>> -Wes
>>
>> > Try printing out the string containing solvopt in mmpbsa_energy.nab,
>> so
>> > something like this:
>> >
>> > fprintf(stderr, "solvopt=%d, accept=%lf, maxitn=%d, fillratio=%lf,
>> > space=%lf",
>> > pbopt.solvopt, pbopt.accept, pbopt.maxitn,
>> pbopt.fillratio,
>> > pbopt.space))
>> >
>> > prior to sending the string to the mm_options call, just to make sure
>> that
>> > the string is what it appears to be.
>> >
>> >
>> > On Fri, Feb 22, 2013 at 2:27 PM, <wmsmith.uci.edu> wrote:
>> >
>> >> When using
>> >>
>> >> solvopt{Assign}[1-68]
>> >>
>> >> The error message is now reading
>> >> "Error: mm_option: unknown keyword or invalid value: 0,"
>> >> instead of
>> >> "Error: mm_option: unknown keyword or invalid value: solvopt"
>> >> as it did before.
>> >>
>> >> This seems rather strange to me... anyone know why it seems to be
>> >> showing
>> >> "0" as a keyword?
>> >>
>> >> I haven't made any other modifications as of my last post, other than
>> >> changing the one line in mm_options.l to read as shown above.
>> >>
>> >> -Wes
>> >>
>> >> > On Thu, Feb 21, 2013, wmsmith.uci.edu wrote:
>> >> >> Here were the relevant source file changes (as of last try):
>> >> >> -mm_options.l, Line 160
>> >> >> solvopt{Assign}[1-6]|8 { ECHO; solvopt =
>> >> setVarInt(yytext);
>> >> >> }
>> >> >
>> >> > Try this:
>> >> >
>> >> > solvopt{Assign}[1-68]
>> >> >
>> >> > [If you really want to use the "|", you have to use parentheses to
>> >> > establish
>> >> > precendence: solvopt{Assign}([1-6]|8).]
>> >> >
>> >> > ...dac
>> >> >
>> >> > _______________________________________________
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>> >> > AMBER-Developers.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>> >> >
>> >> >
>> >>
>> >>
>> >> _______________________________________________
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>> >>
>> >
>> >
>> >
>> > --
>> > 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
>> >
>> >
>>
>>
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>
>
>
> --
> 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
>
>
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Received on Fri Feb 22 2013 - 14:30:02 PST
