[AMBER] Differences on MMPBSA calculation results

From: MarcZhang <progress0935zhang.gmail.com>
Date: Mon, 19 Oct 2015 16:58:57 +0200

Dear Amber user group

 

I found differences on my MMPBSA calculation results, when I tried to
reproduce the results in the Amber tutorial.

 

The binding free energy of Ras-Raf was calculated using the exact input
files and trajectory files from the tutorial. (AMBER ADVANCED TUTORIALS
TUTORIAL 3 - SECTION 3.1)

 

The calculation results suggested that MMGBSA returned decent values but
results of MMPBSA were far deviated from the values given in the tutorial.

 

The only differences I found in the results file is that my calculation used
mmpbsa_py_energy PBSA solver instead of sander in tutorial.

 

Is this the reason for the deviations? How can I change the solver, if it is
cause.

 

Thank you very much for your help!

 

Cheers

 

 

Here is the my calculation results:

| Run on Mon Oct 19 14:16:21 2015

|

|Input file:

|--------------------------------------------------------------

|Input file for running PB and GB

|&general

| endframe=50, verbose=1,

|# entropy=1,

|/

|&gb

| igb=2, saltcon=0.100

|/

|&pb

| istrng=0.100,

|/

|--------------------------------------------------------------

|MMPBSA.py Version=13.0

|Solvated complex topology file: ras-raf_solvated.prmtop

|Complex topology file: ras-raf.prmtop

|Receptor topology file: ras.prmtop

|Ligand topology file: raf.prmtop

|Initial mdcrd(s): prod.mdcrd

|

|Receptor mask: ":1-166"

|Ligand mask: ":167-242"

|

|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                  -1863.7981               16.9946
2.4034
EEL                     -17200.7406               75.1582
10.6290
EGB                      -3249.6527               64.5827
9.1334
ESURF                       91.3567                1.3775
0.1948
 
G gas                   -19064.5387               73.4400
10.3860
G solv                   -3158.2960               64.1112
9.0667
 
TOTAL                   -22222.8347               39.9219
5.6458
 
 
Receptor:
Energy Component            Average              Std. Dev.   Std. Err. of
Mean
----------------------------------------------------------------------------
---
VDWAALS                  -1268.1869               14.0928
1.9930
EEL                     -11557.0789               71.0248
10.0444
EGB                      -2532.0576               57.1271
8.0790
ESURF                       64.2856                1.1041
0.1561
 
G gas                   -12825.2658               66.1471
9.3546
G solv                   -2467.7721               56.9614
8.0556
 
TOTAL                   -15293.0379               32.1381
4.5450
 
 
Ligand:
Energy Component            Average              Std. Dev.   Std. Err. of
Mean
----------------------------------------------------------------------------
---
VDWAALS                   -529.3073                9.3319
1.3197
EEL                      -4684.4887               35.7985
5.0627
EGB                      -1688.9704               26.2775
3.7162
ESURF                       37.0477                0.6113
0.0865
 
G gas                    -5213.7960               37.0299
5.2368
G solv                   -1651.9227               26.1219
3.6942
 
TOTAL                    -6865.7187               22.1937
3.1387
 
 
Differences (Complex - Receptor - Ligand):
Energy Component            Average              Std. Dev.   Std. Err. of
Mean
----------------------------------------------------------------------------
---
VDWAALS                    -66.3039                4.2329
0.5986
EEL                       -959.1730               34.5550
4.8868
EGB                        971.3753               32.7146
4.6265
ESURF                       -9.9766                0.3725
0.0527
 
DELTA G gas              -1025.4769               34.3707
4.8607
DELTA G solv               961.3987               32.5152
4.5983
 
DELTA TOTAL                -64.0781                6.3096
0.8923
 
 
----------------------------------------------------------------------------
---
----------------------------------------------------------------------------
---
 
POISSON BOLTZMANN:
 
Complex:
Energy Component            Average              Std. Dev.   Std. Err. of
Mean
----------------------------------------------------------------------------
---
VDWAALS                  -1863.7981               16.9946
2.4034
EEL                     -17200.7406               75.1582
10.6290
EPB                      -3190.9098               65.7247
9.2949
ENPOLAR                   1933.4589                6.8742
0.9722
EDISPER                  -1134.8693                6.9333
0.9805
 
G gas                   -19064.5387               73.4400
10.3860
G solv                   -2392.3202               64.9746
9.1888
 
TOTAL                   -21456.8589               44.3294
6.2691
 
 
Receptor:
Energy Component            Average              Std. Dev.   Std. Err. of
Mean
----------------------------------------------------------------------------
---
VDWAALS                  -1268.1869               14.0928
1.9930
EEL                     -11557.0789               71.0248
10.0444
EPB                      -2471.4166               55.7345
7.8820
ENPOLAR                   1323.4880                5.2717
0.7455
EDISPER                   -791.2302                4.6135
0.6525
 
G gas                   -12825.2658               66.1471
9.3546
G solv                   -1939.1588               54.5734
7.7178
 
TOTAL                   -14764.4246               36.1469
5.1119
 
 
Ligand:
Energy Component            Average              Std. Dev.   Std. Err. of
Mean
----------------------------------------------------------------------------
---
VDWAALS                   -529.3073                9.3319
1.3197
EEL                      -4684.4887               35.7985
5.0627
EPB                      -1664.1943               27.4311
3.8793
ENPOLAR                    660.9497                3.2883
0.4650
EDISPER                   -445.7195                3.9547
0.5593
 
G gas                    -5213.7960               37.0299
5.2368
G solv                   -1448.9641               27.7526
3.9248
 
TOTAL                    -6662.7601               26.7643
3.7850
 
 
Differences (Complex - Receptor - Ligand):
Energy Component            Average              Std. Dev.   Std. Err. of
Mean
----------------------------------------------------------------------------
---
VDWAALS                    -66.3039                4.2329
0.5986
EEL                       -959.1730               34.5550
4.8868
EPB                        944.7011               33.8872
4.7924
ENPOLAR                    -50.9787                1.8037
0.2551
EDISPER                    102.0803                2.6804
0.3791
 
DELTA G gas              -1025.4769               34.3707
4.8607
DELTA G solv               995.8027               33.8122
4.7818
 
DELTA TOTAL                -29.6742                7.9567
1.1252
 
 
----------------------------------------------------------------------------
---
----------------------------------------------------------------------------
---
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Received on Mon Oct 19 2015 - 08:30:03 PDT
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