Hi Oliver,
The patch has been created. This will most likely break some of the tests,
and I'll have to redo those, but the standard deviations should be correct
now (hopefully). Here's the patch. Move the patch to $AMBERHOME and apply
it via the following:
patch -p0 -N < mmpbsa.patch.3
Thanks!
Jason
On Fri, Jun 25, 2010 at 9:45 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Jun 25 2010 - 07:30:03 PDT
