Re: [AMBER] MMGBSA vs MMPBSA

From: Aronica, Pietro <pietro.aronica07.imperial.ac.uk>
Date: Wed, 7 Dec 2016 02:14:13 +0000

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 Tue Dec 06 2016 - 18:30:02 PST
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