I'm trying to get mmpbsa to work with decomposition and had some doubts
regarding the calculation
I'm running stability calculations as I'm using a 3 seperate trajectory
protocol of Complex, ligand and receptor, with idecomp set to 2.
When looking at the output for the csv formatted out file, there is no
non-polar contribution. Also, the main out file does not contain the
ECAVITY term which I thought would be present.
-------------------------
Total Energy Decomposition:
Frame #,Residue,Internal,van der Waals,Electrostatic,Polar
Solvation,Non-Polar Solv.,TOTAL
1,1,26.618,0.625,-16.661,-24.606,0.0,-14.024
1,2,25.738,-1.37,-78.138,-10.987,0.0,-64.757
1,3,21.565,-2.844,-6.229,-2.373,0.0,10.119
1,4,22.034,-3.03,-38.102,-7.327,0.0,-26.425
1,5,22.635,-5.288,-15.233,1.403,0.0
------------------------
------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 556.1778 0.0000
0.0000
ANGLE 1605.5522 0.0000
0.0000
DIHED 2159.4046 0.0000
0.0000
VDWAALS -1510.9681 0.0000
0.0000
EEL -13465.2254 0.0000
0.0000
1-4 VDW 694.3113 0.0000
0.0000
1-4 EEL 8986.9329 0.0000
0.0000
EPB -2022.8033 0.0000
0.0000
ENPOLAR 38828.3752 0.0000
0.0000
EDISPER -922.9310 0.0000
0.0000
G gas -973.8147 0.0000
0.0000
G solv 35882.6409 0.0000
0.0000
TOTAL 34908.8262 0.0000
0.0000
------------------------------------------------------------------------------
I'm using Amber12 with AmberTools13. My input file is as follows:
----------------------------------------------------------
&general
startframe=1, endframe=4000, interval=4,
verbose=2, keep_files=0, debug_printlevel=3,netcdf=1,
receptor_mask="1-198", ligand_mask="199",
verbose=2,
/
######################################################
&pb
istrng=0.15, fillratio=4.0,
cavity_offset=0.92, cavity_surften=0.00542,
exdi=80.0, indi=1.0,
radiopt=1,
/
######################################################
&decomp
idecomp=2, dec_verbose=3,
print_res="1-198, 199",
/
----------------------------------------------------------
Could someone help as to how to calculate the nonpolar contribution using
the stability run method?
Many thanks!
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Received on Mon Jul 29 2013 - 16:30:02 PDT
