Please be careful about these values, they should reflect the method you
are trying to use. All MMPBSA defaults are for inp=2, therefore you
should carefully search for the correct values for inp=1. Only ignore
warnings when you know very well what you are doing.
If you search the AMBER list archives, you should be able to find an
email from me that contains the values for inp=1. You can also check the
original publication. If unsuccessful, I will look them up later and get
back to you.
Best
Vlad
On 10/20/2015 12:19 PM, Fabian gmail wrote:
> Hi Jason,
>
> I followed your suggestion and set radiopt=0 and inp=1 in your &pb section and try again… but there are warnings when running MMPBSA.py regarding the inp=1 which I don’t understand… (please see below). The energies are much more similar to the tutorial.
>
> Are then those parameters you suggested the correct ones despite teh warnings?
>
> All the details below.
>
> Thanks lot,
>
> Fabian
>
> Here is the input file modified as you suggested
>
> Input file for running PB and GB
> &general
> verbose=1,
> entropy=0,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> radiopt=0, inp=1
> /
>
>
>
> And here is the output and the warnings I get when I run it with my own mdcrd file (10 ns in this case):
>
>
>
> ==> MMPBSA.py -O -i mmpbsa_2b.in -o FINAL_RESULTS_MMPBSA.dat -sp 1err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y *.mdcrd
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /Users/admin/Data/TOOLS/amber14/bin/mmpbsa_py_energy
> cpptraj found! Using /Users/admin/Data/TOOLS/amber14/bin/cpptraj
> Preparing trajectories for simulation...
> 50 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /Users/admin/Data/TOOLS/amber14/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
> Beginning PB calculations with /Users/admin/Data/TOOLS/amber14/bin/mmpbsa_py_energy
> calculating complex contribution...
> 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
> calculating receptor contribution...
> 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
> calculating ligand contribution...
> 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
>
> Timing:
> Total setup time: 0.035 min.
> Creating trajectories with cpptraj: 0.293 min.
> Total calculation time: 16.376 min.
>
> Total GB calculation time: 2.464 min.
> Total PB calculation time: 13.912 min.
>
> Statistics calculation & output writing: 0.000 min.
> Total time taken: 16.706 min.
>
>
> 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
>
>
> But the energies are correct this time.
>
>
> Here is the FINAL_RESULTS_MMPBSA.dat file
>
>
>
> | Run on Tue Oct 20 13:11:30 2015
> |
> |Input file:
> |--------------------------------------------------------------
> |Input file for running PB and GB in serial
> |&general
> | endframe=50, keep_files=2,
> |/
> |&gb
> | igb=2, saltcon=0.100,
> |/
> |&pb
> | istrng=0.100,
> | radiopt=0, inp=1
> |/
> |--------------------------------------------------------------
> |MMPBSA.py Version=14.0
> |Solvated complex topology file: 1err.solvated.prmtop
> |Complex topology file: complex.prmtop
> |Receptor topology file: receptor.prmtop
> |Ligand topology file: ligand.prmtop
> |Initial mdcrd(s): 1err_prod.mdcrd
> |
> |Receptor mask: ":1-240"
> |Ligand mask: ":241"
> |Ligand residue name is "RAL"
> |
> |Calculations performed using 50 complex frames.
> |Poisson Boltzmann calculations performed using internal PBSA solver in mmpbsa_py_energy
> |
> |Generalized Born ESURF calculated using 'LCPO' surface areas
> |
> |All units are reported in kcal/mole.
> -------------------------------------------------------------------------------
> -------------------------------------------------------------------------------
>
> GENERALIZED BORN:
>
> Complex:
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -2013.3861 20.1108 2.8441
> EEL -16938.6434 84.8707 12.0025
> EGB -3506.9860 67.1003 9.4894
> ESURF 97.4744 1.3170 0.1863
>
> G gas -18952.0295 81.3542 11.5052
> G solv -3409.5116 66.5951 9.4180
>
> TOTAL -22361.5411 36.3100 5.1350
>
>
> Receptor:
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -1955.2346 19.0529 2.6945
> EEL -16895.0333 84.6812 11.9757
> EGB -3528.7058 67.6664 9.5695
> ESURF 101.2621 1.2926 0.1828
>
> G gas -18850.2679 80.7202 11.4156
> G solv -3427.4437 67.2065 9.5044
>
> TOTAL -22277.7116 34.9512 4.9428
>
>
> Ligand:
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -1.8595 2.0320 0.2874
> EEL -5.5800 2.0133 0.2847
> EGB -28.4852 0.5979 0.0846
> ESURF 4.4805 0.0425 0.0060
>
> G gas -7.4395 3.0299 0.4285
> G solv -24.0047 0.6040 0.0854
>
> TOTAL -31.4442 3.2513 0.4598
>
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -56.2921 2.8956 0.4095
> EEL -38.0301 3.1822 0.4500
> EGB 50.2050 2.5622 0.3624
> ESURF -8.2682 0.2700 0.0382
>
> DELTA G gas -94.3222 3.3476 0.4734
> DELTA G solv 41.9369 2.4569 0.3475
>
> DELTA TOTAL -52.3853 2.4400 0.3451
>
>
> -------------------------------------------------------------------------------
> -------------------------------------------------------------------------------
>
> POISSON BOLTZMANN:
>
> Complex:
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -2013.3861 20.1108 2.8441
> EEL -16938.6434 84.8707 12.0025
> EPB -3314.8738 66.2632 9.3710
> ENPOLAR 63.9049 0.4744 0.0671
>
> G gas -18952.0295 81.3542 11.5052
> G solv -3250.9688 66.1312 9.3524
>
> TOTAL -22202.9984 38.5993 5.4588
>
>
> Receptor:
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -1955.2346 19.0529 2.6945
> EEL -16895.0333 84.6812 11.9757
> EPB -3340.9508 66.5434 9.4107
> ENPOLAR 65.6147 0.4833 0.0684
>
> G gas -18850.2679 80.7202 11.4156
> G solv -3275.3361 66.4327 9.3950
>
> TOTAL -22125.6040 37.0760 5.2433
>
>
> Ligand:
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -1.8595 2.0320 0.2874
> EEL -5.5800 2.0133 0.2847
> EPB -30.7649 0.6756 0.0955
> ENPOLAR 3.8717 0.0261 0.0037
>
> G gas -7.4395 3.0299 0.4285
> G solv -26.8932 0.6809 0.0963
>
> TOTAL -34.3327 3.2575 0.4607
>
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -56.2921 2.8956 0.4095
> EEL -38.0301 3.1822 0.4500
> EPB 56.8420 2.9272 0.4140
> ENPOLAR -5.5814 0.1540 0.0218
> EDISPER 0.0000 0.0000 0.0000
>
> DELTA G gas -94.3222 3.3476 0.4734
> DELTA G solv 51.2605 2.9326 0.4147
>
> DELTA TOTAL -43.0617 2.8642 0.4051
>
>
> -------------------------------------------------------------------------------
> -------------------------------------------------------------------------------
>
> ____________________
> Dr. Fabian Glaser
>
> Head of the Structural Bioinformatics section
>
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
>
> fglaser at technion dot ac dot il
> Tel: +972 4 8293701
> http://bku.technion.ac.il
>
>
>> On 19 Oct 2015, at 6:24 PM, Jason Swails <jason.swails.gmail.com> wrote:
>>
>> That's because in the time between when the tutorial was written and the
>> current version of the code, the default nonpolar solvation model changed,
>> unfortunately. If you compare the *polar* solvation free energy component
>> (EPB), you *should* find that they are very similar.
>>
>> Indeed, if you compare them, the tutorial lists 57.6402 kcal/mol as the
>> polar solvation free energy of binding, while your output gives 56.7534
>> kcal/mol. I don't know why the discrepancy is as large as 1.1 kcal/mol,
>> but it's certainly a lot smaller than 35 kcal/mol.
>>
>> If you want to recover the original tutorial results (or values close to
>> it), set radiopt=0 and inp=1 in your &pb section and try again. I really
>> should try to find some time to update the tutorial...
>>
>> Hope this helps,
>> Jason
>>
>> On Mon, Oct 19, 2015 at 10:17 AM, Fabian gmail <fabian.glaser.gmail.com <mailto:fabian.glaser.gmail.com>>
>> wrote:
>>
>>> Dear Amber colleagues,
>>>
>>> I am doing all the MMPBSA tutorials, and I found consistently that while
>>> the GENERALISED BORN results are almost identical to the tutorial (using
>>> the tutorial .mdrcd and .prmtop files) the POISSON BOLTZMANN results are
>>> completely different. As I said I only did the MMPBSA.py calculation, using
>>> given files. For example using the following command for tutorial files A
>>> 3.2 (
>>> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm <http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm> <
>>> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm <http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm>>)
>>> I got the following FINAL_RESULTS_MMPBSA.dat file, which as you see for
>>> the POISSON BOLTZMANN yields a much lower DELTA TOTAL -6.6887 compared to
>>> the tutorial DELTA G binding = -41.7256 !!
>>>
>>> Why is that?????
>>>
>>> As explained above the GENERALISED BORN results are much more similar, for
>>> my calculation is DELTA TOTAL -52.3853 and the tutorial is
>>> DELTA G binding = -52.2672. That is great.
>>>
>>> I used the command and input files provided on the tutorial:
>>>
>>> MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
>>> 1err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
>>> ligand.prmtop -y *.mdcrd
>>>
>>> I want to test this method on several systems, so it’s important for me to
>>> understand the differences…. any hint will really help me. The same happens
>>> on 3.1 so I suspect there is something different or wrong with the
>>> calculation.
>>>
>>> Thanks a lot in advance,
>>>
>>> Fabian
>>>
>>> ____________________
>>> Dr. Fabian Glaser
>>>
>>> Head of the Structural Bioinformatics section
>>>
>>> Bioinformatics Knowledge Unit - BKU
>>> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
>>> Engineering
>>> Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
>>>
>>> fglaser at technion dot ac dot il
>>> Tel: +972 4 8293701
>>> http://bku.technion.ac.il
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>>> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
>>>
>>
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Tue Oct 20 2015 - 05:00:03 PDT
