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.
For each complex I have run 20 simulations. There's a coordinated water
molecule between receptor and ligand that is spacially conserved during the
simulation.
I'm calculating three MMPBSA variants:
1. water not included in the calculation
2. water part of the ligand
3. water part of the receptor
This works fine for five out of six complexes.
For the sixth one, only variant 1 is working and I get output like this for
2 and 3 for receptor and ligand:
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,
complex traj was completely written .
_MMPBSA_ptraj2.out says:
PTRAJ: Successfully read in 199 sets and processed 199 sets. - which is not
ok, somethings wrong writing rec and lig.
same with _MMPBSA_ptraj3.out
I run into this problem for all 20 simulations.
I can imagine that this is a common problem, - please tell me if you need
any more information.
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 - 13:30:03 PDT
