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
> >> >
> >> > _______________________________________________
> >> > AMBER-Developers mailing list
> >> > AMBER-Developers.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >> >
> >> >
> >>
> >>
> >> _______________________________________________
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> >> 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
> >
> >
>
>
> _______________________________________________
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> 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
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Received on Fri Feb 22 2013 - 13:30:03 PST
