George,
I suppose you can see all these terms with the normal mmpbsa run
without the pairwise decomposition option? If not, please share with
us your input and output files.
Ray
On Wed, Jul 31, 2013 at 4:08 PM, George Green <soyo.green.gmail.com> wrote:
> 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!
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Wed Jul 31 2013 - 03:00:03 PDT
