Dear Amber users,
I have a query on the results obtained from mmgbsa
calculation using Amber12. Please let me know your thoughts on this.
I ran a mmgbsa and residue decomposition calculation on snapshots
extracted from a protein-peptide simulation using mmpbsa.py. The input
script file is:
-------------------------------------------------------------------------------------------------
sample input file for MM-GBSA calculation and DECOMPOSITION
&general
startframe=1, endframe=500, interval=1,
verbose=2, keep_files=2,
/
&gb
igb=2, saltcon=0.100,
/
&decomp
idecomp=2,
dec_verbose=0,
csv_format=0,
/
---------------------------------------------------------------------------------------------------
The enthaply of binding computed with equivalent number of snapshots
extracted from the beginning and end of the simulation is:
BEGINNING:
---------------------------------------------------------------------------------------------------
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
BOND 0.0000 0.0001 0.0000
ANGLE 0.0000 0.0000 0.0000
DIHED -0.0000 0.0000 0.0000
VDWAALS -55.5023 5.1859 0.2319
EEL -362.0986 37.5069 1.6774
1-4 VDW 0.0000 0.0000 0.0000
1-4 EEL 0.0000 0.0001 0.0000
EGB 382.1887 36.7726 1.6445
ESURF -9.7307 0.4481 0.0200
DELTA G gas -417.6008 37.9138 1.6956
DELTA G solv 372.4580 36.7059 1.6415
DELTA TOTAL -45.1429 3.9792 0.1780
---------------------------------------------------------------------------------------------------
END:
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 -61.7292 5.5762 0.2491
EEL -643.4552 46.3428 2.0704
1-4 VDW -0.0000 0.0000 0.0000
1-4 EEL -0.0000 0.0001 0.0000
EGB 648.0102 42.7014 1.9078
ESURF -10.4951 0.4444 0.0199
DELTA G gas -705.1844 48.0748 2.1478
DELTA G solv 637.5151 42.4987 1.8987
DELTA TOTAL -67.6693 7.2110 0.3222
--------------------------------------------------------------------------------------------------
The difference in enthalpy is -22.526 Kcal/mol
Now I compare the residue-wise decomposition between the same set of
snapshots highlighting only the residues from the peptide.
BEGINNING:
Residue | Location | Internal | van der Waals |
Electrostatic | Polar Solvation | Non-Polar Solv. |
TOTAL
-------------------------------------------------------------------------------------------------------------------------------------------------------
191 | L 2 | 0.000 +/- 0.000 | -0.817 +/- 0.385 | -29.342
+/- 8.225 | 30.197 +/- 7.773 | -0.137 +/- 0.104 | -0.098 +/-
0.727
192 | L 3 | 0.000 +/- 0.000 | -5.088 +/- 0.780 | -38.756
+/- 5.484 | 41.639 +/- 5.749 | -0.832 +/- 0.071 | -3.037 +/-
0.844
193 | L 4 | 0.000 +/- 0.000 | -5.119 +/- 0.828 | -67.319
+/- 7.263 | 67.990 +/- 6.957 | -0.841 +/- 0.090 | -5.289 +/-
1.020
194 | L 5 | 0.000 +/- 0.000 | -2.500 +/- 0.542 | -2.283
+/- 1.007 | 3.259 +/- 0.830 | -0.447 +/- 0.043 | -1.970 +/-
0.607
195 | L 6 | 0.000 +/- 0.000 | -0.981 +/- 0.226 | 0.283
+/- 0.853 | 0.918 +/- 0.907 | -0.091 +/- 0.044 | 0.130 +/-
0.204
196 | L 7 | 0.000 +/- 0.000 | -2.933 +/- 1.160 | -44.347
+/- 4.216 | 41.099 +/- 3.416 | -0.897 +/- 0.109 | -7.079 +/-
1.403
197 | L 8 | 0.000 +/- 0.000 | -0.368 +/- 0.069 | 3.529
+/- 0.633 | -3.412 +/- 0.627 | -0.002 +/- 0.006 | -0.253 +/-
0.089
198 | L 9 | 0.000 +/- 0.000 | -1.801 +/- 0.569 | -0.056
+/- 0.629 | 1.023 +/- 0.755 | -0.284 +/- 0.132 | -1.117 +/-
0.471
199 | L 10 | 0.000 +/- 0.000 | -1.987 +/- 0.580 | -2.575
+/- 0.841 | 2.771 +/- 0.771 | -0.520 +/- 0.051 | -2.311 +/-
0.472
200 | L 11 | 0.000 +/- 0.000 | -0.985 +/- 0.324 | 0.766
+/- 0.784 | -0.076 +/- 0.859 | -0.137 +/- 0.064 | -0.432 +/-
0.223
201 | L 12 | 0.000 +/- 0.000 | -0.536 +/- 0.332 | -2.256
+/- 1.398 | 2.544 +/- 1.286 | -0.036 +/- 0.070 | -0.284 +/-
0.195
202 | L 13 | 0.000 +/- 0.000 | -3.754 +/- 1.027 | 0.812
+/- 1.271 | 1.648 +/- 1.287 | -0.749 +/- 0.171 | -2.042 +/-
0.897
END:
Residue | Location | Internal | van der Waals |
Electrostatic | Polar Solvation | Non-Polar Solv. |
TOTAL
-------------------------------------------------------------------------------------------------------------------------------------------------------
191 | L 2 | 0.000 +/- 0.000 | -2.698 +/- 0.753 | -46.270
+/- 8.485 | 49.124 +/- 8.950 | -0.466 +/- 0.117 | -0.310 +/-
0.715
192 | L 3 | 0.000 +/- 0.000 | -3.529 +/- 1.065 | -110.573
+/- 9.513 | 108.684 +/- 8.564 | -0.875 +/- 0.057 | -6.293 +/-
1.288
193 | L 4 | 0.000 +/- 0.000 | -4.402 +/- 1.121 | -109.169
+/- 10.965 | 102.732 +/- 9.003 | -0.779 +/- 0.081 | -11.618 +/-
2.140
194 | L 5 | 0.000 +/- 0.000 | -3.641 +/- 0.522 | -0.438
+/- 0.947 | 0.658 +/- 0.830 | -0.666 +/- 0.054 | -4.087 +/-
0.493
195 | L 6 | 0.000 +/- 0.000 | -1.217 +/- 0.261 | -0.412
+/- 1.397 | 2.322 +/- 1.631 | -0.077 +/- 0.052 | 0.616 +/-
0.359
196 | L 7 | 0.000 +/- 0.000 | -2.895 +/- 1.062 | -45.153
+/- 4.600 | 43.499 +/- 3.964 | -0.813 +/- 0.080 | -5.363 +/-
1.597
197 | L 8 | 0.000 +/- 0.000 | -1.108 +/- 0.275 | 0.214
+/- 0.565 | 0.245 +/- 0.595 | -0.125 +/- 0.050 | -0.774 +/-
0.225
198 | L 9 | 0.000 +/- 0.000 | -5.670 +/- 0.683 | -2.761
+/- 0.642 | 5.300 +/- 0.542 | -0.840 +/- 0.126 | -3.971 +/-
0.628
199 | L 10 | 0.000 +/- 0.000 | -1.413 +/- 0.480 | -1.893
+/- 0.493 | 2.514 +/- 0.599 | -0.226 +/- 0.057 | -1.019 +/-
0.378
200 | L 11 | 0.000 +/- 0.000 | -0.169 +/- 0.056 | -1.514
+/- 0.286 | 1.723 +/- 0.275 | -0.000 +/- 0.001 | 0.040 +/-
0.041
201 | L 12 | 0.000 +/- 0.000 | -0.605 +/- 0.167 | -3.950
+/- 0.660 | 3.889 +/- 0.661 | -0.083 +/- 0.039 | -0.750 +/-
0.216
202 | L 13 | 0.000 +/- 0.000 | -2.946 +/- 1.444 | -0.542
+/- 1.384 | 2.492 +/- 0.898 | -0.607 +/- 0.244 | -1.603 +/-
0.846
If we compare the last "TOTAL" column between the two set of
calculations, the total difference computed comes to about -12.214
Kcal/mol.
If we compare this with the total enthalpy difference between the
whole peptide and that of the individual residues it is (-22.256
-(-12.214)) -10.042 Kcal/mol
I thought this has to even out and be zero. Why is -10 Kcal/mol of
energy not accounted for in the two calcultions??
Sorry if I have missed out some basic idea or information. Can someone
please give some insight on this??
Thank you,
Dilraj.
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Received on Fri Aug 23 2013 - 04:00:02 PDT
