OK, thanks, Dr. Swails.
After the change, in the script, from npopt to inp the message disappears;
on the other hand, I will start looking into the python version.
J.
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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Received on Wed Oct 05 2011 - 05:30:02 PDT
