If you have AmberTools 12 installed, you can try MMPBSA.py instead. You're
using an old version of mm_pbsa.pl which many developers may not even have
easy access to anymore.
If you want to try debugging this, start with an input file from the
Examples directory that corresponds to the closest type of calculation you
want to attempt and use that as-is to make sure it works. Then, try
changing that input file to match your options one at a time until you find
the error. (Do this with only two frames or so to save time).
HTH,
Jason
On Thu, Nov 15, 2012 at 2:32 AM, Anogna <anognal.gmail.com> wrote:
> Dear Amber Users,
>
> I try to calculate free-energy calculations using MMPBSA method for my
> complex protein.
>
> I have done with First part of the process. i.e, Minimization,
> equilibration and Production.
>
> When i proceed with MMPBSA step, I modified mm_pbsa.in file as per my
> requirements and i run using mm_pbsa.pl file.
>
> The command i used : *mm_pbsa.pl mm_pbsa.in > mm_pbsa.log*
>
> But the process stopped showing the following statement.
>
> *Can't use an undefined value as an ARRAY reference at
>
> /applications/smp/amber/10/intelmpi-mkl/src/mm_pbsa/mm_pbsa_statistics.pmline
> 953.
> Can't use an undefined value as an ARRAY reference at
>
> /applications/smp/amber/10/intelmpi-mkl/src/mm_pbsa/mm_pbsa_statistics.pmline
> 953.
> Can't use an undefined value as an ARRAY reference at
>
> /applications/smp/amber/10/intelmpi-mkl/src/mm_pbsa/mm_pbsa_statistics.pmline
> 953.
> Can't use an undefined value as an ARRAY reference at
>
> /applications/smp/amber/10/intelmpi-mkl/src/mm_pbsa/mm_pbsa_statistics.pmline
> 953.
> Can't use an undefined value as an ARRAY reference at
>
> /applications/smp/amber/10/intelmpi-mkl/src/mm_pbsa/mm_pbsa_statistics.pmline
> 953.
> not opened
> Can't use an undefined value as an ARRAY reference at
>
> /applications/smp/amber/10/intelmpi-mkl/src/mm_pbsa/mm_pbsa_statistics.pmline
> 953.
> Can't use an undefined value as an ARRAY reference at
>
> /applications/smp/amber/10/intelmpi-mkl/src/mm_pbsa/mm_pbsa_statistics.pmline
> 953.
> Can't use an undefined value as an ARRAY reference at
>
> /applications/smp/amber/10/intelmpi-mkl/src/mm_pbsa/mm_pbsa_statistics.pmline
> 953.
> Can't use an undefined value as an ARRAY reference at
>
> /applications/smp/amber/10/intelmpi-mkl/src/mm_pbsa/mm_pbsa_statistics.pmline
> 953.
> *
>
> Can anyone help me with this please.
>
> With regards,
> Anogna
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Nov 16 2012 - 05:00:02 PST
