Dear Amber community,
there is a huge difference between the GB and PB energy values I have
calculated for the same trajectory
My system consists of protein-cofactor-inhibitor-4 zinc atoms.
I have treated Zn atoms in the cationic dummy atom method according to the
tutorial.
MD simulations are fine.
IN MMPBSA calculation I treated "protein-cofactor-4 zinc atoms" as
"Receptor" and "Inhibitor" as "Ligand"
Initially, I have faced an error on PB calculation which I have solved with
"radiopt=0" flag.
Later, MMPBSA calculations are also running smoothly. In the end, I saw
that the large energy difference in the calculated energy.
my input file looks like this
=======================================
|due GB and PB decomposition
|&general
| startframe=1, interval=1, verbose=1,
|/
|&gb
| igb=5, saltcon=0.100,
|/
|&pb
| istrng=0.100, radiopt=0,
|/
|&decomp
| idecomp=1,
| dec_verbose=1,
|/
*=======================================*
and, output file looks like this
===================================================
|
|Calculations performed using 5000 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
sander.
|
|Generalized Born ESURF calculated using 'LCPO' surface areas
GENERALIZED BORN:
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -46.3374 3.5124
0.0497
EEL -257.7393 17.0368
0.2409
EGB 271.0342 16.7361
0.2367
ESURF -5.9403 0.3135
0.0044
DELTA G gas -304.0766 18.4957
0.2616
DELTA G solv 265.0939 16.5853
0.2346
DELTA TOTAL -38.9828 5.8140
0.0822
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -46.3374 3.5124
0.0497
EEL -257.7393 17.0368
0.2409
EPB 277.7781 16.9461
0.2397
ENPOLAR -33.2217 1.6110
0.0228
EDISPER 53.4479 1.8152
0.0257
DELTA G gas -304.0766 18.4957
0.2616
DELTA G solv 298.0043 17.0231
0.2407
DELTA TOTAL -6.0724 5.6593
0.0800
-------------------------------------------------------------------------------
=================================================
what is the reason for this, Is this because of I selected radii from
.prmtop itself for PB calculation?
If so how can I calculate reliable values?
Is there any other or alternate options?
--
*-Regards-*
*ம. ரம்ய சந்தர் சார்லஸ்(M.Ramya Chandar Charles*)
Research Scholar
c/o Dr. S. Mohane Coumar
Centre for Bioinformatics
Pondicherry university
Mob: +91-9283684619
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Received on Fri Jul 06 2018 - 01:00:01 PDT
