Hi All,
After recent upgrade to Amber 16 I wanted to calculate very simply thing.
Binding energy between Br anion and Dodecyltrimethylammonium in
Dodecyltrimethylammonium bromide molecular complex
( see
http://www.sigmaaldrich.com/catalog/product/sigma/d5047?lang=en®ion=CZ
).
I used MMPBSA.py.MPI for this calculation (6 threads).
I tried #1 GB calculation #2 PB calculation and #3 TdS calucaltion
(entropic contribution).
Interestingly I succeeded just in case of GB calculation the rest was
finished
with errors.
I am naturally asking why ? and what to try to do to eliminate those
errors.
Please see input/output files below and thank you in advance for your
suggestions.
In case of PB calculation I have obtained errors which were printed
directly to the screen
----------------------------------------
/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py:631:
UserWarning: Solvated topology 0 has IFBOX == 0
warn('Solvated topology %s has IFBOX == 0' % ifbox)
Warning: inp=1 was old default
Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
inp=1 default value: 0.0050
Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
inp=1 default value: 0.000
Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
value: 1.400
Warning: inp=1 was old default
Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
inp=1 default value: 0.0050
Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
inp=1 default value: 0.000
Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
value: 1.400
Warning: inp=1 was old default
Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
inp=1 default value: 0.0050
Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
inp=1 default value: 0.000
Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
value: 1.400
Warning: inp=1 was old default
Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
inp=1 default value: 0.0050
Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
inp=1 default value: 0.000
Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
value: 1.400
Warning: inp=1 was old default
Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
inp=1 default value: 0.0050
Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
inp=1 default value: 0.000
Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
value: 1.400
Warning: inp=1 was old default
Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
inp=1 default value: 0.0050
Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
inp=1 default value: 0.000
Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
value: 1.400
File "/opt/amber16/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 431, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /opt/amber16/bin/mmpbsa_py_energy failed with prmtop
../../prmtop/COM.prmtop!
----------------------------------------
I would like just to notice that All 3 calculations are using identical
set of promtop files
(COM.prmtop, LIG.prmtop, REC.prmtop) which are in one central folder.
In case of TdS calculation I have obtained errors which were printed
directly to the screen
----------------------------------------------
ERROR in xmin(): Too few atoms.
ERROR in xmin(): Too few atoms.
ERROR in xmin(): Too few atoms.
ERROR in xmin(): Too few atoms.
ERROR in xmin(): Too few atoms.
ERROR in xmin(): Too few atoms.
File "/opt/amber16/bin/MMPBSA.py.MPI", line 108, in <module>
app.parse_output_files()
File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 942, in parse_output_files
self.INPUT['verbose'], self.using_chamber)
File
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py",
line 999, in __init__
self.delta2()
File
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py",
line 1232, in delta2
self.lig.data[key].avg(),
File
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py",
line 187, in avg
return (sum(self) / len(self))
ZeroDivisionError: integer division or modulo by zero
Error occured on rank 0.
Exiting. All files have been retained.
----------------------------------------------
This suggests that routine xmin() has problem with 1-atom residues (here
Ligand Br-).
There is clearly missing this trivial branch which simply in such cases
does not apply any
minimization (because there is nothing to minimize at all in such case)
and just return the input "configuration".
I would like just to notice that the similar problems I had when I wanted
to
calculate binding energy between complete "Dodecyltrimethylammonium
bromide"
complex and another molecule. The following rows indicates that if part
of analysed system is/are ion/ions i.e. 1-atom residuum, there might be
problems (PB, TdS calc.) also because some procedures simply do not count
with such cases.
Thank you in advance !
Best wishes,
Marek
INPUT/OUTPUT files
#1 - GB
INPUT (mmpbsa.in)
-----------------------------------------
MMPBSA.py input file for running GB
&general
interval=10,startframe=1
keep_files=1, debug_printlevel=2
/
&gb
igb=1, saltcon=0.0
/
--------------------------------------------
OUTPUT (mmpbsa.out)
-------------------------------------------
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/amber16/bin/mmpbsa_py_energy
cpptraj found! Using /opt/amber16/bin/cpptraj
Preparing trajectories for simulation...
100 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /opt/amber16/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Timing:
Total setup time: 0.016 sec.
Creating trajectories with cpptraj: 0.048 sec.
Total calculation time: 0.066 sec.
Total GB calculation time: 0.061 sec.
Statistics calculation & output writing: 0.005 sec.
Total time taken: 0.146 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
-------------------------------------------
#2 - PB
INPUT (mmpbsa.in)
-----------------------------------------
MMPBSA input file for running PB
&general
interval=10,startframe=1
keep_files=1, debug_printlevel=2
/
&pb
istrng=0.0, inp=1,
radiopt=0, exdi=1,
/
#&decomp
#cavity_surften=0.00542
#idecomp=2, dec_verbose=0
#/
--------------------------------------------
OUTPUT (mmpbsa.out)
-------------------------------------------
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/amber16/bin/mmpbsa_py_energy
cpptraj found! Using /opt/amber16/bin/cpptraj
Preparing trajectories for simulation...
100 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /opt/amber16/bin/mmpbsa_py_energy
calculating complex contribution...
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 16649 RUNNING AT dyn-138-272.ujep.cz
= EXIT CODE: 1
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
-------------------------------------------
#3 - TdS
INPUT (mmpbsa.in)
-----------------------------------------
MMPBSA input file for running per-residue decomp
&general
startframe=1
keep_files=1, debug_printlevel=2,
/
&nmode
nmode_igb=0, nmode_istrng=0.0, nminterval=167,
maxcyc=10000, drms=0.1,
/
--------------------------------------------
OUTPUT (mmpbsa.out)
-------------------------------------------
Loading and checking parameter files for compatibility...
cpptraj found! Using /opt/amber16/bin/cpptraj
mmpbsa_py_nabnmode found! Using /opt/amber16/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
1000 frames were processed by cpptraj for use in calculation.
6 frames were processed by cpptraj for nmode calculations.
Running calculations on normal system...
Beginning nmode calculations with /opt/amber16/bin/mmpbsa_py_nabnmode
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 16821 RUNNING AT dyn-138-272.ujep.cz
= EXIT CODE: 1
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
-------------------------------------------
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Tue Nov 01 2016 - 09:00:02 PDT
