Apologies! please ignore the last email. We were playing with the script and
left a modified utils.py version in $AMBERHOME/bin. After fixing python
version issues I reinstalled but the utils.pyc script generated in
$AMBERHOME/bin was of course ignored by python in favour of our broken
utils.py
On 25 June 2010 09:58, Oliver Grant <olivercgrant.gmail.com> wrote:
> 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
> <module>
> 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
> '',finaloutput,debug,numframes,sander_apbs,one_trajectory,verbose)
> File "/array2/programs/amber11_20100607/bin/utils.py", line 2150, in
> pboutput
> diffstdev.append(stdev(diff_dif, diffavg[0])) #change
>
>
>
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Received on Fri Jun 25 2010 - 04:30:03 PDT
