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
>> ===================================================================================
>>
>> -------------------------------------------
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>> http://www.opera.com/mail/
>>
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>
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Received on Tue Nov 01 2016 - 11:00:04 PDT
