Re: [AMBER] mmpbsa nonpolar contribution using stability calculations

From: Ray Luo <rayhuangluo.gmail.com>
Date: Tue, 30 Jul 2013 10:18:45 +0800

George,

I don't think the no polar term in PB can be decomposed into pair wise terms. Only the GB version can be done so far.

Ray Luo, Ph.D.

On 2013-7-30, at 7:08, George Green <soyo.green.gmail.com> wrote:

> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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Received on Mon Jul 29 2013 - 19:30:02 PDT
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