Re: [AMBER] MMPBSA Delta total results

From: Elvis Martis <elvis.martis.bcp.edu.in>
Date: Fri, 7 Jul 2017 02:03:10 +0000

Dear Ray,
Just a correction.
inp=2 is default in amber14 and amber17

Best Regards
Elvis Martis
Mumbai, INDIA.

________________________________________
From: Ray Luo [rluo.uci.edu]
Sent: 07 July 2017 01:04
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA Delta total results

That's because you used inp=2 for pb. If you use inp=1, your pb and gb
energies will be more similar.

Looks like you are using the amber 14 release. The default has been
set to inp=1 in newer releases.

Ray
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Thu, Jul 6, 2017 at 2:49 AM, NADIA RAHMAH <nadiiarah.apps.ipb.ac.id> wrote:
> Sorry to send not complete results. I didnt tell you this is PB Delta G. PB
> Delta total value is positive while GB Delta is negaive, Is it problem or
> something error?
>
> |Input file:
> |--------------------------------------------------------------
> |Sample input file for GB and PB calculation
> |&general
> |startframe=1, endframe=10000, interval=50,
> |verbose=2, keep_files=0,
> |/
> |&gb
> |igb=5, saltcon=0.150,
> |/
> |&pb
> |istrng=0.15, fillratio=4.0
> |/
> |--------------------------------------------------------------
> |MMPBSA.py Version=14.0
> |Complex topology file:           complexnobox_3wi7rbb.prmtop
> |Receptor topology file:          protein.prmtop
> |Ligand topology file:            ligan.prmtop
> |Initial mdcrd(s):                3wi7rbb.nc
> |
> |Receptor mask:                  ":1-291"
> |Ligand mask:                    ":292"
> |Ligand residue name is "UNL"
> |
> |Calculations performed using 200 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
> -------------------------------------------------------------------------------
> BOND                       912.5936               23.3491
> 1.6510
> ANGLE                     2428.7787               34.2154
> 2.4194
> DIHED                     3769.6586               21.4600
> 1.5175
> VDWAALS                  -2466.7203               22.2716
> 1.5748
> EEL                     -19829.1418              106.3164
> 7.5177
> 1-4 VDW                   1084.1896               14.5553
> 1.0292
> 1-4 EEL                   9856.0973               41.1595
> 2.9104
> EGB                      -2557.6201               85.2699
> 6.0295
> ESURF                       89.0527                1.7420
> 0.1232
>
> G gas                    -4244.5444              103.4226
> 7.3131
> G solv                   -2468.5674               84.5367
> 5.9776
>
> TOTAL                    -6713.1118               51.4808
> 3.6402
>
>
> Receptor:
> Energy Component            Average              Std. Dev.   Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> BOND                       911.3783               23.2978
> 1.6474
> ANGLE                     2422.5641               34.0504
> 2.4077
> DIHED                     3768.2360               21.4450
> 1.5164
> VDWAALS                  -2448.4510               22.0682
> 1.5605
> EEL                     -19821.6598              106.3786
> 7.5221
> 1-4 VDW                   1083.3272               14.6062
> 1.0328
> 1-4 EEL                   9857.1039               41.1947
> 2.9129
> EGB                      -2565.1932               85.3334
> 6.0340
> ESURF                       89.9441                1.7262
> 0.1221
>
> G gas                    -4227.5013              104.0079
> 7.3545
> G solv                   -2475.2491               84.5944
> 5.9817
>
> TOTAL                    -6702.7503               51.5860
> 3.6477
>
> Ligand:
> Energy Component            Average              Std. Dev.   Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> BOND                         1.2152                0.9774
> 0.0691
> ANGLE                        6.2146                2.0044
> 0.1417
> DIHED                        1.4225                0.6671
> 0.0472
> VDWAALS                     -0.0078                0.3911
> 0.0277
> EEL                         -0.4298                0.2128
> 0.0150
> 1-4 VDW                      0.8625                0.4192
> 0.0296
> 1-4 EEL                     -1.0066                0.2333
> 0.0165
> EGB                         -2.4506                0.0873
> 0.0062
> ESURF                        1.6260                0.0096
> 0.0007
>
> G gas                        8.2706                2.4641
> 0.1742
> G solv                      -0.8245                0.0865
> 0.0061
>
> TOTAL                        7.4461                2.4730
> 0.1749
>
>
> Differences (Complex - Receptor - Ligand):
> Energy Component            Average              Std. Dev.   Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> BOND                        -0.0000                0.0001
> 0.0000
> ANGLE                        0.0000                0.0001
> 0.0000
> DIHED                        0.0000                0.0000
> 0.0000
> VDWAALS                    -18.2614                1.2729
> 0.0900
> EEL                         -7.0523                1.8874
> 0.1335
> 1-4 VDW                     -0.0000                0.0001
> 0.0000
> 1-4 EEL                     -0.0000                0.0000
> 0.0000
> EGB                         10.0237                1.5415
> 0.1090
> ESURF                       -2.5175                0.0801
> 0.0057
>
> DELTA G gas                -25.3137                2.2277
> 0.1575
> DELTA G solv                 7.5062                1.5431
> 0.1091
>
> DELTA TOTAL                -17.8075                1.8112
> 0.1281
>
>
> -------------------------------------------------------------------------------
> -------------------------------------------------------------------------------
>
> POISSON BOLTZMANN:
>
> Complex:
> Energy Component            Average              Std. Dev.   Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> BOND                       912.5936               23.3491
> 1.6510
> ANGLE                     2428.7787               34.2154
> 2.4194
> DIHED                     3769.6586               21.4600
> 1.5175
> VDWAALS                  -2466.7203               22.2716
> 1.5748
> EEL                     -19829.1418              106.3164
> 7.5177
> 1-4 VDW                   1084.1896               14.5553
> 1.0292
> 1-4 EEL                   9856.0973               41.1595
> 2.9104
> EPB                      -2639.8863               86.9608
> 6.1491
> ENPOLAR                   2191.4591                8.4002
> 0.5940
> EDISPER                  -1130.7876                9.7908
> 0.6923
>
> G gas                    -4244.5444              103.4226
> 7.3131
> G solv                   -1579.2148               86.0073
> 6.0816
>
> TOTAL                    -5823.7592               56.4697
> 3.9930
>
>
> Receptor:
> Energy Component            Average              Std. Dev.   Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> BOND                       911.3783               23.2978
> 1.6474
> ANGLE                     2422.5641               34.0504
> 2.4077
> DIHED                     3768.2360               21.4450
> 1.5164
> VDWAALS                  -2448.4510               22.0682
> 1.5605
> EEL                     -19821.6598              106.3786
> 7.5221
> 1-4 VDW                   1083.3272               14.6062
> 1.0328
> 1-4 EEL                   9857.1039               41.1947
> 2.9129
> EPB                      -2660.8632               86.9206
> 6.1462
> ENPOLAR                   2190.4601                8.3759
> 0.5923
> EDISPER                  -1139.5953                9.7842
> 0.6919
>
> G gas                    -4227.5013              104.0079
> 7.3545
> G solv                   -1609.9985               85.9000
> 6.0740
>
> TOTAL                    -5837.4998               55.4874
> 3.9235
>
> Ligand:
> Energy Component            Average              Std. Dev.   Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> BOND                         1.2152                0.9774
> 0.0691
> ANGLE                        6.2146                2.0044
> 0.1417
> DIHED                        1.4225                0.6671
> 0.0472
> VDWAALS                     -0.0078                0.3911
> 0.0277
> EEL                         -0.4298                0.2128
> 0.0150
> 1-4 VDW                      0.8625                0.4192
> 0.0296
> 1-4 EEL                     -1.0066                0.2333
> 0.0165
> EPB                         -2.2980                0.0776
> 0.0055
> ENPOLAR                     14.9804                0.1359
> 0.0096
> EDISPER                    -13.3213                0.0859
> 0.0061
>
> G gas                        8.2706                2.4641
> 0.1742
> G solv                      -0.6389                0.1582
> 0.0112
>
> TOTAL                        7.6317                2.4782
> 0.1752
>
>
> Differences (Complex - Receptor - Ligand):
> Energy Component            Average              Std. Dev.   Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> BOND                        -0.0000                0.0001
> 0.0000
> ANGLE                        0.0000                0.0001
> 0.0000
> DIHED                        0.0000                0.0000
> 0.0000
> VDWAALS                    -18.2614                1.2729
> 0.0900
> EEL                         -7.0523                1.8874
> 0.1335
> 1-4 VDW                     -0.0000                0.0001
> 0.0000
> 1-4 EEL                     -0.0000                0.0000
> 0.0000
> EPB                         23.2749                5.0209
> 0.3550
> ENPOLAR                    -13.9814                0.2315
> 0.0164
> EDISPER                     22.1291                0.5543
> 0.0392
>
> DELTA G gas                -25.3137                2.2277
> 0.1575
> DELTA G solv                31.4226                5.0797
> 0.3592
>
> DELTA TOTAL                  6.1089                4.1135
> 0.2909
>
>
>
>
>
>
> On Thu, Jul 6, 2017 at 4:27 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
>> HI,
>> I assume this delta G is the results of either PB or GB calculations.
>> In the absence of entropy calculations, this delta G total reflects only
>> the enthalpy component and hence not the true delta G binding.
>>
>> Best Regards
>> Elvis Martis
>> Mumbai, INDIA.
>>
>> ________________________________________
>> From: NADIA RAHMAH <nadiiarah.apps.ipb.ac.id>
>> Sent: 06 July 2017 12:45:40
>> To: AMBER Mailing List
>> Subject: [AMBER] MMPBSA Delta total results
>>
>> Hello Amber Users, I want to ask about MMPBSA results, at the end of the
>> results, I get DELTA TOTAL :
>>
>> DELTA G gas                -24.9391                2.2411
>> 0.1585
>> DELTA G solv                34.0352                3.5423
>> 0.2505
>>
>> DELTA TOTAL                  9.0961                3.7742
>> 0.2669
>>
>> I want to ask, is DELTA TOTAL same with Delta G Binding? because I dont
>> find Delta G Binding in my results. and the delta total value is so
>> positive. Thanks
>> --
>>
>> *Regards,*
>> *Nadia Rahmah*
>> *Department of Physics Undergraduate Student - 2013Bogor Agricultural
>> University*
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
>
> *Regards,*
> *Nadia Rahmah*
> *Department of Physics Undergraduate Student - 2013Bogor Agricultural
> University*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 06 2017 - 19:30:03 PDT
Custom Search