Hello,
Just to point out, you can use the same command to run MMPBSA.py, but run
with -rewrite-output, and it will simply re-compile the output files without
having to re-do the calculation. I just say this because 100 frames may
take a while to recalculate.
Thanks!
Jason
On Fri, Jun 25, 2010 at 7:12 AM, Oliver Grant <olivercgrant.gmail.com>wrote:
> 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
> >
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 25 2010 - 07:00:03 PDT
