Dear Amber users,
I am performing MM/PBSA calculation with idecomp =1 per-residue
decomposition option on my protein-ligand system. The ligand is a small
organic molecule.
Just to be curious, I summed up decomposed per-residue energies, then I
found the Eelec from decomposed file doesn't add up to the number reported
in the final averaged result file...
Below is averaged final result file:
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 -37.0580 4.0991
0.0826*
*EEL -12.9451 2.5435
0.0512*
1-4 VDW 0.0000 0.0000
0.0000
1-4 EEL -0.0000 0.0000
0.0000
*EPB 15.8420 1.8276
0.0368*
*ENPOLAR -5.8373 0.5390
0.0109*
EDISPER 0.0000 0.0000
0.0000
DELTA G gas -50.0031 3.9687
0.0799
DELTA G solv 10.0047 1.9391
0.0391
*DELTA TOTAL -39.9984 3.8605
0.0778*
--------------------------------------------------------------------------------------------------------------------------------------------------------------
Below is the decomposed file that I processed and summarized receptor
residues (1-99) and lig (100):
--------------------------------------------------------------------------------------------------------------------------------------------------------------
DELTAS:
Total Energy Decomposition:
Residue Location Internal *van der Waals Electrostatic*
*Polar Solvation
Non-Polar Solv. TOTAL*
*BAZ 100* L BAZ 1 0 0 0 *-18.52900487* 2.049551273 0.041281011 *-25.89016349
*5.086963618 0.102459013 *7.385438945* 0.907196193 0.018272281* 0* 0 0
*-37.03372941* 3.942699281 0.079411828
*Receptor 1-99 * summed up *-18.52890548*
*-25.89008235* *8.456529817*
*-35.96245801*
--------------------------------------------------------------------------------------------------------------------------------------------------------------
I highlighted the energy components. It seems like the EvdW is decomposed
with half to receptor and half to ligand. And I know non-polar is not
decomposable in MMPBSA. It seems like the EPB could be added up, too...
But then the Eelec part seems to be the double of the average....Maybe I am
missing some of the background knowledge of decomposition here or the
electrostatic energy calculation...? Or, I double counted Electrostatic
contribution when I directly summing up receptor residues 1-99? But all the
other components seem to add up well... Can anyone explain a little bit to
me?
Thanks for the help!!!
-Guqin
--
Guqin SHI
PhD Candidate in Medicinal Chemistry and Pharmacognosy
College of Pharmacy
The Ohio State University
Columbus, OH, 43210
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Received on Mon Sep 04 2017 - 17:30:02 PDT
