Hi Jason,
I have a somewhat peculiar problem within the MMPBSA.py script.
I have run the same procedure on six complexes and it works for five, but
not the sixth one.
There I get:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.4537E+08 6.1154E+04 1.7462E+05 C5 22
BOND = ************* ANGLE = 8242.9732 DIHED =
277.6273
VDWAALS = -0.0479 EEL = -25.8709 EPB =
-937.6616
1-4 VDW = -0.0000 1-4 EEL = 1.1064 RESTRAINT =
0.0000
ENPOLAR = 41.1862
So I looked into the ptraj.out files:
_MMPBSA_ptraj1.out says:
PTRAJ: Successfully read in 200 sets and processed 200 sets. - that's ok
_MMPBSA_ptraj2.out says:
PTRAJ: Successfully read in 199 sets and processed 199 sets. - which is not
ok
same with _MMPBSA_ptraj3.out
So, why is there one 'frame' lost?
I can imagine that this is a common problem, - please tell me if you need
any more information.
btw, this problem occurs in context with treating one (spacially conserved)
water as part of ligand or as part of the receptor.
This works for the other five complexes and also the calculation that does
not include this water works for this complex.
Regards,
Oliver
--
Oliver Kuhn, Department of Bioinformatics,
Center for Medical Biotechnology, University of Duisburg-Essen,
Universitätsstr. 1-5, 45141 Essen, Germany
phone +49 201 183-3121, oliver.kuhn.uni-due.de
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Received on Mon May 16 2011 - 07:30:03 PDT
