Charles,
Looking at your input script, you seem to be using mostly defaults for the
two methods. This explains the discrepency in the surface area energy terms.
For pbsa, the default is inp=2, which decomposes the non-polar solvation
energy term into a cavity term (ENPOLAR) and a dispersion term (EDISPER).
This differs significantly from the default non-polar solvation method used
by GBSA, which is simply a linear function of the surface area.
You would likely get a closer agreement if you use inp=1 for PBSA. It would
then compute the nonpolar contribution as a single term that is a linear
function of surface area, which is more consistent with the method used in
GBSA.
On Fri, Jul 6, 2018 at 12:55 AM, Charles Mariasoosai <
charlesmariasoosai51.gmail.com> wrote:
> 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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>
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Received on Fri Jul 06 2018 - 12:30:02 PDT
