Re: [AMBER] problem with MMPBSApy in Amber 16 from Marek Maly on 2016-11-01 (Amber Archive Nov 2016)

From: Marek Maly <marek.maly.ujep.cz>
Date: Tue, 01 Nov 2016 23:20:40 +0100

OK, thanks !

Best wishes,

Marek

Dne Tue, 01 Nov 2016 22:34:01 +0100 Ray Luo <rluo.uci.edu> napsal/-a:

> Marek,
>
> Looks like the timer function is not reset properly when imin=5 AND
> epsin=epsout, which causes skipping of many routines.
>
> Will submit a patch this week.
>
> Thanks a lot for reporting this!
>
> 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 1:29 PM, Ray Luo <rluo.uci.edu> wrote:
>> Okay, I'm looking at your data file to reproduce the problem ...
>>
>> 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 12:14 PM, Marek Maly <marek.maly.ujep.cz> wrote:
>>> 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&region=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 - 15:30:03 PDT