I think the problem was because of the version of amber12 on the cluster.
Solved the "raise CalcError" issue by using another install.
However, there is still no ECAVITY term in the outfile after removing the
decomposition parts and setting "radiopt=0" which is very puzzling.
The invocation I am using to call the program is:
MMPBSA.py -O -i ../mmpbsa.in -o 01_ALA_01_net_01.out -cp
../../../../ALA_01_mmpbsa_leap/ProtLigOnly_mmpbsa_ALA_Bound_mbondi.parm -y
../../../../01_ALA_01_Traj/md_01.net 1> output.txt 2> error.txt
######################################
There is the following error from stdout: errors.txt.
-------------------------------------------------------------------------
An MPI process has executed an operation involving a call to the
"fork()" system call to create a child process. Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your MPI job may hang, crash, or produce silent
data corruption. The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.
The process that invoked fork was:
Local host: clus6847.jaq (PID 114362)
MPI_COMM_WORLD rank: 0
If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
--------------------------------------------------------------------------
######################################
The program output: output.txt:
Loading and checking parameter files for compatibility...
Preparing trajectories for simulation...
2 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /export/progs/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
Timing:
Total setup time: 2.246 sec.
Creating trajectories with cpptraj: 1.679 sec.
Total calculation time: 30.871 sec.
Total PB calculation time: 30.871 sec.
Statistics calculation & output writing: 0.042 sec.
Total time taken: 34.939 sec.
MMPBSA.py Finished! Thank you for using. Please cite us if you publish this
work with this paper:
Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke,
H. and Roitberg, A. E.
J. Chem. Theory Comput., 2012, 8 (9) pp 3314--3321
mmpbsa_py_energy found! Using /export/progs/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /export/progs/amber12/bin/cpptraj
###################################
My outfile is:
|Input file:
|--------------------------------------------------------------
|#Sample input file for GB and PB calculation
|&general
|startframe=1, endframe=4000, interval=2000,
|verbose=2, keep_files=0, debug_printlevel=3,netcdf=1,
|receptor_mask="1-198", ligand_mask="199",
|/
|&pb
|istrng=0.15, fillratio=4.0,
|inp=2,
|cavity_offset=0.92, cavity_surften=0.00542,
|exdi=80.0, indi=1.0,
|radiopt=0,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=13.0
|Complex topology file:
../../../../ALA_Complex_mmpbsa_leap/ProtLigOnly_noBox_mmpbsa_ALA_Bound_mbondi.parm
|Initial mdcrd(s): ../../../../01_ALA_Complex_Traj/md_25.net
|
|Calculations performed using 2 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
mmpbsa_py_energy
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 558.7818 10.6091
7.5018
ANGLE 1562.8214 46.3017
32.7403
DIHED 2154.2506 6.7232
4.7540
VDWAALS -1506.6383 7.0408
4.9786
EEL -13456.6047 96.4087
68.1713
1-4 VDW 678.0244 4.0240
2.8454
1-4 EEL 9000.3978 30.3358
21.4506
EPB -2135.3337 85.9077
60.7459
ENPOLAR 229.5122 0.4394
0.3107
EDISPER -959.3307 0.5602
0.3961
G gas -1008.9671 119.2775
84.3419
G solv -2865.1523 86.0284
60.8313
TOTAL -3874.1193 33.2490
23.5106
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
This is all the output data that has been obtained. The error is prob
because its installed on
the cluster and I didn't compile openmpi as it is already on the cluster.
However, I'm not using
mpi, so not sure how important this error is?
The current version of Amber and AmberTools that is being used is also up
to date.
AmberTools version 13.15
Amber version 12.18
Any suggestions would be very welcome, as I'm not sure what I've done wrong.
Thanks
On Thu, Aug 1, 2013 at 9:20 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Aug 1, 2013 at 4:44 PM, George Green <soyo.green.gmail.com> wrote:
>
> > Ok, I'm now getting a really weird problem that has got me scratching my
> > head. If I take the decomposition parameters out of the mmpbsa.in file,
> > the
> > script fails with the following error:
> >
> > ----------------------------------------
> > File
> "/apps/applications/amber/12/1/default/amber12/bin.real/MMPBSA.py",
> > line 565, in ?
> > external_progs, '_MMPBSA_', normal_system)
> > File
> >
> >
> "/apps1/applications/amber/12/1/default/amber12/bin/MMPBSA_mods/calculation.py",
> > line 176, in run_calculations
> > calc.Run()
> > File
> >
> >
> "/apps1/applications/amber/12/1/default/amber12/bin/MMPBSA_mods/calculation.py",
> > line 664, in Run
> > raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> > CalcError:
> > /apps/applications/amber/12/1/default/amber12/bin/mmpbsa_py_energy failed
> > with prmtop
> >
> >
> ../../../../ALA_Complex_mmpbsa_leap/ProtLigOnly_mmpbsa_ALA_Bound_mbondi.parm!
> >
>
> Is this the whole stderr stream? It would help to have the output and
> error streams, since the error message might be in one of those.
>
>
> >
> >
> > Exiting. All files have been retained.
> > ----------------------------------------
> >
> >
> >
> > The _MMPBSA_complex_pb.mdout.0 file has the following info:
> > [snip]
> >
>
>
> >
> > The mmpbsa.in file is as follows:
> > -----------------------------------------------------
> > #Sample input file for GB and PB calculation
> > &general
> > startframe=1, endframe=4000, interval=2000,
> > verbose=2, keep_files=0, debug_printlevel=3,netcdf=1,
> > /
> >
> > &pb
> > istrng=0.15, fillratio=4.0,
> > cavity_offset=0.92, cavity_surften=0.00542,
> > exdi=80.0, indi=1.0,
> > radiopt=1,
> >
> >
> > /
> >
>
> radiopt=1 means use optimized radii. There are quite a few cases where
> this does not work because some of your atom types may not be supported by
> this model. Setting radiopt=0 often fixes this issue. But this diagnosis
> is pure speculation since your output files didn't have enough information
> to help me.
>
> Also make sure that your AmberTools 13 is fully up-to-date.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 19 2013 - 03:30:02 PDT
