Dear AMBERs,
I use MM-PBSA script from AMBER 6.0 package for inhibitor/protein free
binding energy estimation. Today I noticed that the E(internal) =
E(int, complex) - E(int, protein) - E(int, ligand) significantly differs
from 0 value, but there was no covalent bond between ligand and protein. I
think that it doesn't make sence. Where could be the mistake?
Thank you very much for your suggestions,
Michal Otyepka
----------------------------------------------------------------------------------
Complex (AB) Receptor (A) Ligand
(B)
Contribution ----------------------- ----------------------
----------------------
mean std mean std mean
std
----------------------------------------------------------------------------------
Eelectrostat -7735.1259 73.3700 -7465.3016 73.1727 -255.6492
2.7423
EvdW -1312.0442 26.3638 -1271.2495 26.3603 7.8156
1.5214
Einternal 5204.9836 39.3425 5165.1632 37.7177 44.7937
4.9476
Egas -3842.1864 75.5490 -3571.3879 74.4260 -203.0400
4.5009
E(nonpolar) 81.8064 0.7202 83.1195 0.7552 4.4408
0.0574
E(PB) -4078.6113 57.8883 -4098.4525 56.6599 -17.6948
0.7014
E(solvation) -3996.8049 57.6374 -4015.3330 56.4062 -13.2539
0.7015
E(PB+elect) -11813.7372 35.5400 -11563.7542 34.8206 -273.3440
2.4695
E(total,PB) -7838.9913 38.1928 -7586.7209 37.0649 -216.2939
4.3522
E(nonpolGB) 107.4506 0.9568 109.1949 1.0032 4.6771
0.0763
E(GB) -4124.4346 68.7497 -4157.9450 67.6094 -16.7118
0.7598
E(solvation) -4016.9840 68.4860 -4048.7501 67.3374 -12.0347
0.7679
E(GB+elect) -11859.5605 29.9890 -11623.2466 29.0456 -272.3610
2.4591
E(total,GB) -7859.1704 32.8283 -7620.1379 32.1150 -215.0747
4.5338
----------------------------------------------------------------------------------
Interactions [AB-(A+B)]
------------------------------------
Contribution mean std
------------------------------------
Eelectrostat -14.1750 3.4873
EvdW -48.6103 2.8162
Egas -67.7586 3.9524
E(nonpolar) -5.7539 0.1680
E(PB) 37.5360 3.0671
E(solvation) 31.7821 3.0116
E(PB+elect) 23.3610 4.3720
E(total,PB) -35.9765 4.3916
E(nonpolGB) -6.4214 0.2232
E(GB) 50.2222 4.3387
E(solvation) 43.8008 4.3184
E(GB+elect) 36.0472 5.2100
E(total,GB) -23.9578 5.0043
------------------------------------
*---------------------------------------------[*]-*
| Department of Inorganic and Physical Chemistry |
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| |
|ph. +420 68 563 4756 fax +420 68 522 5737|
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|
http://aix.upol.cz/~otyepka |
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*-------------------------------------------------*
Received on Wed Oct 10 2001 - 09:58:19 PDT
