Dr. Green,
Yes, in the latest patched versions, the ECAVITY term should be absent
from the mmpbsa summary file if you used default settings.
>From what I can tell, it looks like the latest patched versions renamed
ECAVITY as ENPOLAR (at least when radiopt is set to 0 and default inp is
used). You can verify this by checking the mdout file and the mmpbsa
output summary.
When radiopt is set to zero mmpbsa_py gives consistent summary results for
the most current versions of amber12 and amber13. I should have the patch
ready to make the default consistent by this evening.
Finally, the "G solv" and "G gas" terms in the mmpbsa output are the sums
of the EPB, ENPOLAR (ECAVITY) and EDISPER terms for the solvated and
vacuum (gas) systems respectively.
I did see some odd behaviour with the ECAVITY term showing up with a value
of 0 in an older unpatched amber12, but the most recent patches seem to
have taken care of this.
-Wesley Botello-Smith
---------- Forwarded message ----------
From: George Green <soyo.green.gmail.com>
Date: Mon, Aug 19, 2013 at 3:07 AM
Subject: Re: [AMBER] mmpbsa nonpolar contribution using stability
calculations
To: AMBER Mailing List <amber.ambermd.org>
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 Tue Aug 20 2013 - 09:30:04 PDT
