Thanks for the information. I was unaware that the non polar contribution
could not be decomposed on a per-residue basis.
However, how is it calculated normally from a stability calculation? There
is no ECAVITY or SASA term in the main outfile (i.e the bit that is not
decomposed). I only get the following output:
------------------------------------------------------------------------------
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
------------------------------------------------------------------------------
When calculating the non polar term previously when not using sander alone
without the mmpbsa.py script , I used the formula (SASA *surften) +
surfOff. I am unsure as to how to proceed with only the EDISPER term.
Thanks again.
On Tue, Jul 30, 2013 at 2:18 AM, Ray Luo <rayhuangluo.gmail.com> wrote:
> 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 上午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!
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jul 31 2013 - 01:30:02 PDT
