[AMBER] Problem in mmpbsa calculation

From: Rakesh Roy <royrakesh8900.gmail.com>
Date: Mon, 10 Jan 2022 11:16:47 +0530

Dear all,
I am facing troubles in mmpbsa calculation of a protein ligand system, the
delta G value is hugely possitive ..
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 10428.3213 93.6642
31.2214
ANGLE 23704.4713 53.7951
17.9317
DIHED 38663.6749 77.2044
25.7348
VDWAALS -22904.3818 64.5204
21.5068
EEL -208380.0311 271.1143
90.3714
1-4 VDW 50751.3083 773.8533
 257.9511
1-4 EEL 124292.5019 163.7082
54.5694
EPB -34799.7615 211.6926
70.5642
ENPOLAR 718.4198 2.7619
 0.9206

G gas 16555.8648 780.9280
 260.3093
G solv -34081.3417 209.3751
69.7917

TOTAL -17525.4769 740.0495
 246.6832


Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 10393.6746 97.2016
32.4005
ANGLE 23624.7843 54.1698
18.0566
DIHED 38567.7552 76.3694
25.4565
VDWAALS -22841.4257 64.1243
21.3748
EEL -208147.4289 273.5621
91.1874
1-4 VDW 10876.5611 45.9864
15.3288
1-4 EEL 124099.1216 163.4024
54.4675
EPB -34822.1131 207.8732
69.2911
ENPOLAR 719.8613 2.6703
 0.8901

G gas -23426.9578 306.0712
 102.0237
G solv -34102.2518 205.6683
68.5561

TOTAL -57529.2096 167.8521
55.9507

Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 34.6467 7.2570
 2.4190
ANGLE 79.6870 7.6537
 2.5512
DIHED 95.9196 3.4456
 1.1485
VDWAALS -4.5243 2.8538
 0.9513
EEL -174.6294 13.6975
 4.5658
1-4 VDW 7919.4752 760.3606
 253.4535
1-4 EEL 198.6071 6.4554
 2.1518
EPB -84.2920 5.3367
 1.7789
ENPOLAR 4.9870 0.0519
 0.0173

G gas 8149.1819 765.9106
 255.3035
G solv -79.3050 5.3177
 1.7726

TOTAL 8069.8769 766.2696
 255.4232


Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND -0.0000 0.0000
 0.0000
ANGLE -0.0000 0.0000
 0.0000
DIHED 0.0000 0.0000
 0.0000
VDWAALS -58.4318 3.0394
 1.0131
EEL -57.9728 15.9504
 5.3168
1-4 VDW 31955.2720 0.8193
 0.2731
1-4 EEL -5.2267 0.1454
 0.0485
EPB 106.6436 10.7497
 3.5832
ENPOLAR -6.4285 0.1968
 0.0656
EDISPER 0.0000 0.0000
 0.0000

DELTA G gas 31833.6407 14.5462
 4.8487
DELTA G solv 100.2151 10.6462
 3.5487

DELTA TOTAL 31933.8558 7.3172
 2.4391

Any suggestions from your side..


Thanking you


*Rakesh Kumar Roy,*
*Junior Research Fellow,*
Department Of Applied Chemistry,
IIT (ISM) Dhanbad,
Dhanbad-826004, Jharkhand, INDIA.
Contact no. 8709383084, 8877544146

email- royrakesh8900.gmail.com
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Received on Sun Jan 09 2022 - 22:00:02 PST
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