Hi Users,
I am using Amber 12 and a similarly old version of mmpbsa.py to perform
energy calculations for protein-ligand complex binding. RMSD and vmd
visualizations of trajectory showed NO unusual behavior. However the
results of the MMPBSA calculation gave a delta total= 1414.7 kcal/mole.
This is my first time performing energy calculations (using a very old
version). I have followed the tutorial given on amber tutorial site and I
have included the parameters inp=1, radiopt=0 in the &pb section of the
input file (this was recommended for older versions). Could there be
something I am missing in my procedure that's leading to this highly
positive binding energy?
The mmpbsa result is given here:
| Run on Sat Oct 12 09:42:02 2019
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
| startframe=2500, endframe=3000, interval=5, keep_files=2, verbos=2,
|/
|&pb
| istrng=0.100, inp=1, radiopt=0,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=12.0
|Solvated complex topology file: ../complex.prmtop
|Complex topology file: complex_nowater.prmtop
|Receptor topology file: receptor.prmtop
|Ligand topology file: ligand.prmtop
|Initial mdcrd(s): ../prod1.mdcrd
|
|Receptor mask: ":1-293"
|Ligand mask: ":294"
|Ligand residue name is "UNK"
|
|Calculations performed using 101 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
mmpbsa_py_energy
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 457518.3870 19442.5193
1934.6030
ANGLE 7137.6181 81.7575
8.1352
DIHED 3388.7612 36.1528
3.5973
VDWAALS 1283943.5303 13956.9637
1388.7698
EEL -21121.4699 97.4144
9.6931
1-4 VDW 13084.2238 1510.9414
150.3443
1-4 EEL 10460.6128 42.3240
4.2114
EPB -3932.7319 90.9624
9.0511
ENPOLAR -15580.6284 201.4230
20.0423
G gas 1754411.6633 23190.2210
2307.5132
G solv -19513.3603 263.2498
26.1943
TOTAL 1734898.3030 23147.7197
2303.2842
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 946.9401 28.4312
2.8290
ANGLE 2539.7637 34.6293
3.4457
DIHED 3208.8062 24.2581
2.4138
VDWAALS -2384.6326 25.9208
2.5792
EEL -21634.3378 96.6331
9.6154
1-4 VDW 1102.9940 12.7919
1.2728
1-4 EEL 10643.9116 42.2768
4.2067
EPB -3560.7359 85.5100
8.5086
ENPOLAR -15752.0704 194.8142
19.3847
G gas -5576.5549 107.4650
10.6932
G solv -19312.8062 259.7333
25.8444
TOTAL -24889.3611 197.2184
19.6240
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 456571.4469 19446.4636
1934.9954
ANGLE 4597.8545 78.1909
7.7803
DIHED 179.9550 24.2866
2.4166
VDWAALS 1286079.4620 13951.3203
1388.2083
EEL 445.5646 11.5086
1.1452
1-4 VDW 11981.2298 1510.7870
150.3289
1-4 EEL -183.2989 4.3609
0.4339
EPB -523.0121 8.4230
0.8381
ENPOLAR -776.2982 5.9968
0.5967
G gas 1759672.2138 23177.1611
2306.2137
G solv -1299.3103 10.6430
1.0590
TOTAL 1758372.9036 23172.6195
2305.7618
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 0.0001
0.0000
VDWAALS 248.7010 212.6220
21.1567
EEL 67.3033 26.9754
2.6842
1-4 VDW 0.0000 0.0000
0.0000
1-4 EEL 0.0000 0.0000
0.0000
EPB 151.0161 36.1622
3.5983
ENPOLAR 947.7402 32.3150
3.2155
EDISPER 0.0000 0.0000
0.0000
DELTA G gas 316.0043 214.5189
21.3454
DELTA G solv 1098.7562 55.6904
5.5414
DELTA TOTAL 1414.7605 208.0203
20.6988
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Your expert advice is much appreciated.
Thank you.
Regards.
Seke
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Received on Sun Oct 13 2019 - 17:00:02 PDT
