Re: [AMBER] MMGBSA vs MMPBSA

From: Ray Luo <rluo.uci.edu>
Date: Wed, 7 Dec 2016 10:01:32 -0800

The NP portion is really small for the final delta G from MMPB/GBSA,
so either parameter is okay, I think ... unless you use inp=2 in
MMPBSA.

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, Dec 6, 2016 at 6:14 PM, Aronica, Pietro
<pietro.aronica07.imperial.ac.uk> wrote:
> Yes, I am not using the same surface tension for both because I am following the recommendations of the manual for GB5 and PB4 respectively (page 699). Should I used different flavours of MMPBSA/MMGBSA? These settings seem to work for all other systems, it is just this one that has given me a peculiar result with PB specifically.
>
> ________________________________
> From: Ray Luo <rluo.uci.edu>
> Sent: 06 December 2016 17:03:46
> To: AMBER Mailing List
> Subject: Re: [AMBER] MMGBSA vs MMPBSA
>
> Pietro,
>
> For the NP part, you are not using the same coefficient ... 5
> cal/mol-A^2 for GB and 7.3 cal/mol-A^2 for PB.
>
> The delta G EPB and EGB are 519 kcal/mol and 505 kcal/mol,
> respectively. They are different but apparently close.
>
> 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 Mon, Dec 5, 2016 at 8:15 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>> hi
>>
>> I don't see anything wrong either. You can try with igb=8 too (recommend to
>> use mbondi2 for GBSA in this case).
>>
>> Hai
>>
>> On Mon, Dec 5, 2016 at 11:10 PM, Aronica, Pietro <
>> pietro.aronica07.imperial.ac.uk> wrote:
>>
>>> Hello,
>>>
>>> I have recently run a simulation of a simple protein receptor + peptide
>>> ligand system and tried to calculate the MMGBSA and MMPBSA difference in
>>> energy between the bound and unbound state.
>>>
>>> In my experience, the absolute value for the PB tends to be a few kcal/mol
>>> lower than the GB one, but in this system this was not the case. While the
>>> GB was -67.7195 ± 5.4461, the PB was -54.7742 ± 11.3891. This is not an
>>> isolated result and the same pattern repeats across different runs. The
>>> discrepancy and the much higher error of the PB give me pause and I have
>>> been looking at the system to determine if something was wrong or if I made
>>> a mistake.
>>>
>>> As far as I can tell I have used all the input files correctly, or at
>>> least in the same way I usually do. What can I be on the lookout for? What
>>> should I check in order to determine the cause of this bizarre result?
>>> Should I even be worried?
>>>
>>> I also print the entire GB and PB output files, in case these are of any
>>> help.
>>>
>>> If there are suggestions or comments, please do let me know.
>>>
>>> Cheers
>>>
>>> Pietro Aronica
>>>
>>>
>>> GB:
>>>
>>> | Run on Tue Dec  6 00:03:58 2016
>>> |
>>> |Input file:
>>> |--------------------------------------------------------------
>>> |&general
>>> |/
>>> |&gb
>>> | igb=5, surften=0.0050
>>> |/
>>> |&decomp
>>> | idecomp=2, dec_verbose=1
>>> |/
>>> |--------------------------------------------------------------
>>> |MMPBSA.py Version=14.0
>>> |Solvated complex topology file:  /home/pietroa/Charge_
>>> derivation/GLU/MMPBSA/FF99SB_KEK_mbondi.prmtop
>>> |Complex topology file:           /home/pietroa/Charge_
>>> derivation/GLU/MMPBSA/FF99SB_KEK_com_mbondi2.prmtop
>>> |Receptor topology file:          /home/pietroa/Charge_
>>> derivation/GLU/MMPBSA/FF99SB_KEK_rec_mbondi2.prmtop
>>> |Ligand topology file:            /home/pietroa/Charge_
>>> derivation/GLU/MMPBSA/FF99SB_KEK_lig_mbondi2.prmtop
>>> |Initial mdcrd(s):                ../Total_run.mdcrd
>>> |
>>> |Receptor mask:                  ":1-517"
>>> |Ligand mask:                    ":518-520"
>>> |
>>> |Calculations performed using 100 complex frames.
>>> |
>>> |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                  -4461.2579               33.9886
>>> 3.3989
>>> EEL                     -39522.6040              144.1058
>>>  14.4106
>>> EGB                      -6004.7227              119.4563
>>>  11.9456
>>> ESURF                       99.6832                2.0092
>>> 0.2009
>>>
>>> G gas                   -43983.8620              147.5266
>>>  14.7527
>>> G solv                   -5905.0395              118.7491
>>>  11.8749
>>>
>>> TOTAL                   -49888.9015               69.0225
>>> 6.9023
>>>
>>>
>>> Receptor:
>>> Energy Component            Average              Std. Dev.   Std. Err. of
>>> Mean
>>> ------------------------------------------------------------
>>> -------------------
>>> VDWAALS                  -4403.5819               33.5620
>>> 3.3562
>>> EEL                     -38747.6831              144.3997
>>>  14.4400
>>> EGB                      -6221.3471              120.6745
>>>  12.0674
>>> ESURF                      103.4116                1.9760
>>> 0.1976
>>>
>>> G gas                   -43151.2651              147.2434
>>>  14.7243
>>> G solv                   -6117.9355              120.0168
>>>  12.0017
>>>
>>> TOTAL                   -49269.2005               68.8915
>>> 6.8892
>>>
>>>
>>> Ligand:
>>> Energy Component            Average              Std. Dev.   Std. Err. of
>>> Mean
>>> ------------------------------------------------------------
>>> -------------------
>>> VDWAALS                     -6.5483                1.2008
>>> 0.1201
>>> EEL                       -258.8440               13.4295
>>> 1.3430
>>> EGB                       -288.8132               12.4559
>>> 1.2456
>>> ESURF                        2.2239                0.0509
>>> 0.0051
>>>
>>> G gas                     -265.3922               12.9580
>>> 1.2958
>>> G solv                    -286.5893               12.4173
>>> 1.2417
>>>
>>> TOTAL                     -551.9815                3.7165
>>> 0.3717
>>>
>>>
>>> Differences (Complex - Receptor - Ligand):
>>> Energy Component            Average              Std. Dev.   Std. Err. of
>>> Mean
>>> ------------------------------------------------------------
>>> -------------------
>>> VDWAALS                    -51.1277                4.2314
>>> 0.4231
>>> EEL                       -516.0770               17.5053
>>> 1.7505
>>> EGB                        505.4375               15.2402
>>> 1.5240
>>> ESURF                       -5.9523                0.1398
>>> 0.0140
>>>
>>> DELTA G gas               -567.2047               16.5366
>>> 1.6537
>>> DELTA G solv               499.4852               15.2016
>>> 1.5202
>>>
>>> DELTA TOTAL                -67.7195                5.4461
>>> 0.5446
>>>
>>>
>>>
>>> PB:
>>>
>>> | Run on Tue Dec  6 08:33:43 2016
>>> |
>>> |Input file:
>>> |--------------------------------------------------------------
>>> |&general
>>> |/
>>> |&pb
>>> | inp=1, radiopt=0, cavity_surften=0.0072
>>> |/
>>> |&decomp
>>> | idecomp=2, dec_verbose=1
>>> |/
>>> |--------------------------------------------------------------
>>> |MMPBSA.py Version=14.0
>>> |Solvated complex topology file:  /home/pietroa/Charge_
>>> derivation/GLU/MMPBSA/FF99SB_KEK_mbondi.prmtop
>>> |Complex topology file:           /home/pietroa/Charge_
>>> derivation/GLU/MMPBSA/FF99SB_KEK_com_mbondi.prmtop
>>> |Receptor topology file:          /home/pietroa/Charge_
>>> derivation/GLU/MMPBSA/FF99SB_KEK_rec_mbondi.prmtop
>>> |Ligand topology file:            /home/pietroa/Charge_
>>> derivation/GLU/MMPBSA/FF99SB_KEK_lig_mbondi.prmtop
>>> |Initial mdcrd(s):                ../Total_run.mdcrd
>>> |
>>> |Receptor mask:                  ":1-517"
>>> |Ligand mask:                    ":518-520"
>>> |
>>> |Calculations performed using 100 complex frames.
>>> |Poisson Boltzmann calculations performed using internal PBSA solver in
>>> sander.
>>> |
>>> |All units are reported in kcal/mole.
>>> ------------------------------------------------------------
>>> -------------------
>>> ------------------------------------------------------------
>>> -------------------
>>>
>>> POISSON BOLTZMANN:
>>>
>>> Complex:
>>> Energy Component            Average              Std. Dev.   Std. Err. of
>>> Mean
>>> ------------------------------------------------------------
>>> -------------------
>>> VDWAALS                  -4461.2579               33.9886
>>> 3.3989
>>> EEL                     -39522.6040              144.1058
>>>  14.4106
>>> EPB                      -5966.1358              119.2844
>>>  11.9284
>>> ENPOLAR                    156.8866                1.7105
>>> 0.1710
>>>
>>> G gas                   -43983.8620              147.5266
>>>  14.7527
>>> G solv                   -5809.2492              118.3545
>>>  11.8354
>>>
>>> TOTAL                   -49793.1112               75.5242
>>> 7.5524
>>>
>>>
>>> Receptor:
>>> Energy Component            Average              Std. Dev.   Std. Err. of
>>> Mean
>>> ------------------------------------------------------------
>>> -------------------
>>> VDWAALS                  -4403.5819               33.5620
>>> 3.3562
>>> EEL                     -38747.6831              144.3997
>>>  14.4400
>>> EPB                      -6196.9759              123.0006
>>>  12.3001
>>> ENPOLAR                    158.8439                1.7092
>>> 0.1709
>>>
>>> G gas                   -43151.2651              147.2434
>>>  14.7243
>>> G solv                   -6038.1320              122.1447
>>>  12.2145
>>> TOTAL                   -49189.3971               72.9118
>>> 7.2912
>>>
>>>
>>> Ligand:
>>> Energy Component            Average              Std. Dev.   Std. Err. of
>>> Mean
>>> ------------------------------------------------------------
>>> -------------------
>>> VDWAALS                     -6.5483                1.2008
>>> 0.1201
>>> EEL                       -258.8440               13.4295
>>> 1.3430
>>> EPB                       -288.9018               12.0239
>>> 1.2024
>>> ENPOLAR                      5.3541                0.0626
>>> 0.0063
>>>
>>> G gas                     -265.3922               12.9580
>>> 1.2958
>>> G solv                    -283.5477               11.9841
>>> 1.1984
>>>
>>> TOTAL                     -548.9399                3.7137
>>> 0.3714
>>>
>>>
>>> Differences (Complex - Receptor - Ligand):
>>> Energy Component            Average              Std. Dev.   Std. Err. of
>>> Mean
>>> ------------------------------------------------------------
>>> -------------------
>>> VDWAALS                    -51.1277                4.2314
>>> 0.4231
>>> EEL                       -516.0770               17.5053
>>> 1.7505
>>> EPB                        519.7418               15.9509
>>> 1.5951
>>> ENPOLAR                     -7.3113                0.1295
>>> 0.0129
>>> EDISPER                      0.0000                0.0000
>>> 0.0000
>>>
>>> DELTA G gas               -567.2047               16.5366
>>> 1.6537
>>> DELTA G solv               512.4305               15.9443
>>> 1.5944
>>>
>>> DELTA TOTAL                -54.7742               11.3891
>>> 1.1389
>>>
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Received on Wed Dec 07 2016 - 10:30:02 PST
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