[AMBER] MMPBSA.py NameError: global name 'diffstdev' is not defined

From: Oliver Grant <olivercgrant.gmail.com>
Date: Fri, 25 Jun 2010 09:58:14 +0100

Hi all,

I checked the archive for this error but no go. I ran this calculation
before with the old version of the script and it worked fine. Any help would
be great. I'm using AMBER11 and python 2.6.

$ MMPBSA.py -i mmpbsa.in -O -o NEW_VERSION_RESULTS -sp sol_complex.top -cp
complex.top -rp pro.top -lp lig.top -y ../../9.ptraj/MD_combined2.crd
ptraj found! Using /array2/programs/amber11_20100607/exe/ptraj
sander found! Using /array2/programs/amber11_20100607/exe/sander

Preparing trajectories with ptraj...
100 frames were read in and processed by ptraj for use in calculation.

Starting calculations...

Starting pb calculation...

  calculating ligand contribution...
  calculating receptor contribution...
  calculating complex contribution...

Calculations complete. Writing output file(s)...

Traceback (most recent call last):
  File "/array2/programs/amber11_20100607/exe/MMPBSA.py", line 1397, in
    decompout, idecomp, dec_verbose, ligstart, decomprun, surften,
cavity_surften, temp)
  File "/array2/proNameError: global name 'diffstdev' is not defined
grams/amber11_20100607/bin/utils.py", line 4696, in PrintFinalResults
  File "/array2/programs/amber11_20100607/bin/utils.py", line 2150, in
    diffstdev.append(stdev(diff_dif, diffavg[0])) #change
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Received on Fri Jun 25 2010 - 02:00:03 PDT
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