Just for the record to close this thread ... Wes Smith was able to run
the job with the data provided. See his email below ... probably Mani
needs to update the package with all the latest patches?
Ray
++++ ++++
Ok, using the rst files you provided, I get MMPBSA.py to run just fine
(after setting the endframe appropriately).
It runs perfectly for the individual rst files. Using VMD I was able to
combine them into a single trajectory as well. The only issue there was
that the box dimensions had to be reset by hand since vmd apparently
doesn't do this right and leaves them all zero.
Once that was done, MMPBSA.py ran just fine with the combined trajectory
as well.
The MMPBSA.py run commands used were:
MMPBSA.py -O -i mmpbsa.in -o mmpbsa_3frame.dat -sp solvated.prmtop -cp
complex.prmtop -rp receptor.prmtop -lp lig.prmtop -y
solvated_3frame_boxfix.traj.crd
and
MMPBSA.py -O -i mmpbsa.in -o mmpbsa.dat -sp solvated.prmtop -cp
complex.prmtop -rp receptor.prmtop -lp lig.prmtop -y md25.rst
Attached are the combined trajectory file and the two dat files created by
MMPBSA.
-mmpbsa.dat = output for first frame only
-mmpbsa_3frame.dat = output for the combined trajectory
-solvated_3frame_boxfix.traj.crd = fixed trajectory file from VMD
I'm not sure what is causing your error. It seems to run fine for me.
Try running it using the attached trajectory file (be sure to set the
endframe to 3 in mmpbsa.in first)
If the error persists then we'll have to see if its due to a bugfix /
patch difference.
-Wes
On Mon, Feb 11, 2013 at 3:24 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Jason,
>
> I got his input and data files and are trying to reproduce his observation ...
>
> Ray
>
> On Mon, Feb 11, 2013 at 2:58 PM, manikanthan bhavaraju
> <mhb75.msstate.edu> wrote:
>> Jason,
>>
>>
>> I have also used MMPBSA.py script of ambertools12 apart from
>> mmpbsa_py_energy from ambetools1.5. Still having the same problem.
>>
>> mani
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 12 2013 - 16:30:02 PST
