Hi Ray,
sorry but keyword "epsout" is not listed as the valid
one for "&pb namelist variables" in MMPBSApy/Amber16 manual.
The only one listed relevant keyword is here "exdi" but anyway
I tried PB calculation with both A) "exdi=1" and B)"epsout=1" with
"use_sander=1".
In case of A) mmpbsa.out stays empty in case of B) the same problem as
in case of using default "mmpbsa_py_energy".
With using sander_apbs it works as I already wrote.
Entropy calc. ends with errors because of the minimization function as you
can
see by yourself when testing my prmtop/mdcrd files.
Best wishes,
Marek
Dne Tue, 01 Nov 2016 18:49:36 +0100 Ray Luo <rluo.uci.edu> napsal/-a:
> Marek,
>
> I can set epsout=1 for pbsa, so I think the option of use_sander
> should work. The default setup uses nab, which is quite limited and is
> hard to trace what went wrong because there is no output recorded.
>
> Ray
> --
> Ray Luo, Ph.D.
> Professor
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Tue, Nov 1, 2016 at 10:36 AM, Marek Maly <marek.maly.ujep.cz> wrote:
>> Thank you Ray,
>>
>> According to Amber16 manual "exdi" is listed only as a
>> MMPBSApy parameter in "&pb namelist variables"
>> not in "&gb namelist variables".
>>
>> So that is the reason why I did not use this parameter
>> in my gb calculation. Anyway pb calculation should work for
>> any value of external el. permitivity const. I guess.
>>
>> Yes for this moment I need just vacuum energy terms so
>> I am OK with gb one because those should be the same
>> for gb and pb but later I will need also calculate
>> energies of systems containing "Dodecyltrimethylammonium bromide"
>> in water.
>>
>> With serial version of MMPBSA (MMPBSA.py) there are identical problems
>> as with the parallel one.
>>
>> I now installed apbs support to have possibility to use sander_apbs
>> with MMPBSA.py environment and it works !
>>
>> But of course would be a good idea to solve this problem also in
>> default Amber PB solver.
>>
>> Moreover there is that problem also for entropy calculation where
>> in the first place should be corrected xmin() procedure.
>>
>> I will send you relevant prmtops/mdcrd files off-line so you can
>> reproduce reported errors and eventually fix it.
>>
>> Best wishes,
>>
>> Marek
>>
>>
>>
>>
>>
>> Dne Tue, 01 Nov 2016 17:14:50 +0100 Ray Luo <rluo.uci.edu> napsal/-a:
>>
>>> Marek,
>>>
>>> I see that you are setting exdi = 1 in PB, but not in GB. Is there any
>>> reason doing so? Do you want to do a vacuum run with PB? What about
>>> the non-MPI run?
>>>
>>> All the best,
>>> Ray
>>> --
>>> Ray Luo, Ph.D.
>>> Professor
>>> Biochemistry, Molecular Biophysics, Chemical Physics,
>>> Chemical and Biomedical Engineering
>>> University of California, Irvine, CA 92697-3900
>>>
>>>
>>> On Tue, Nov 1, 2016 at 8:54 AM, Marek Maly <marek.maly.ujep.cz> wrote:
>>>> 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
>>>> ===================================================================================
>>>>
>>>> -------------------------------------------
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
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>>>> http://www.opera.com/mail/
>>>>
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>>
>> --
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Received on Tue Nov 01 2016 - 12:30:03 PDT
