I think I found them, those are the reccomended parameters?
THANKS!!
FABIAN
cat << EOF > mmpbsa.in
MMPBSA
&general
debug_printlevel=0,
startframe=1,
endframe=50000,
interval=1,
keep_files=1,
netcdf=1,
ligand_mask=":1-152",
receptor_mask=":153-283",
use_sander=1,
entropy=0,
full_traj=1,
verbose=2,
/
&pb
inp=1,
cavity_offset=0.86,
cavity_surften=0.005,
indi=1.0,
exdi=80.0,
fillratio=4.0,
istrng=0.100,
linit=1000,
prbrad=1.4,
radiopt=0,
scale=2.0,
/
EOF
____________________
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 20 Oct 2015, at 2:50 PM, Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
> 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
>
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Oct 20 2015 - 05:30:06 PDT
