I would suggest trying the python version of MM/PBSA. It's included with
AmberTools 1.5 and is more widely supported on this list.
Relating to the variables you're seeing, npopt has been replaced as a
keyword with inp.
HTH,
Jason
On Tue, Oct 4, 2011 at 7:17 PM, Jorge Iulek <jiulek.ig.com.br> wrote:
> Dear all,
>
> I manage to install and compile amber11 and ambertools 1.5. I just
> went to adapt my scripts for these new versions; no big differences
> here. A productive dynamic ran fine, so I went to calculate gbsa/pbsa
> energies, just like in tutorial A3. It runs fine and I do get the
> results as I use to get, but I receive the message:
>
> Use of uninitialized value $inp in concatenation (.) or string at
> /usr/local/amber11+ambertools1_5/amber11/src/mm_pbsa/
> mm_pbsa_createinput.pm
> line 596.
>
> 3 times.
>
> Just comparing mm_pbsa_createinput.pm from amber11 to the one from
> amber10 , at line number 560 of the former I see:
>
> $inp = $r_del->{"INP"};
>
> Compared to the correspondent line of amber10 version:
>
> $npopt = $r_del->{"NPOPT"};
>
> and some other few differences by.
>
> As far as I get the results, how worrisome are the messages? By the
> way, yes, my script to calculate energies is according to the one found
> in tutorial A3.
> Thanks,
>
> Jorge
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Oct 04 2011 - 16:30:04 PDT
