I use gbsa=1 for LCPO model an change the input file using only Generalized
Born with igb=1.What value of surften should I specify here(should I keep
this at default value).
&cntrl
imin=5,
gbsa=1,
surften=1,
igb=1,
ntb=0,
cut=999,
/
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.9428E+04 1.7449E+01 1.0258E+02 C18 1636
BOND = 520.0864 ANGLE = 1565.4763 DIHED =
2393.2239
VDWAALS = -869.2145 EEL = -6041.7483 EGB =
-7126.1713
1-4 VDW = 677.0566 1-4 EEL = 13019.3521 RESTRAINT =
0.0000
ESURF = 15289.9962
minimization completed, ENE= 0.19428057E+05 RMS= 0.174493E+02
minimizing coord set # 6
Maximum number of minimization cycles reached.
To calculate non polar contribution to free energy of solvation(SASA) Enp
= surften*SA ,
Is the surface area represented as ESURF.According to the Generalized born
surface area (SA) is proportional
to the solvation energy of non-polar molecules. Can I obtain the polar
energy contribution .
Thanks
Kirtana
On Tue, Apr 10, 2012 at 12:33 AM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> On Apr 9, 2012, at 9:33 PM, kirtana S <skirtana4.gmail.com> wrote:
>
> > I used sander with igb=10 ( to activate pbsa calculation as in manual)
> with
> > vacuum trajectory with ions and solvent removed.
> >
> > &cntrl
> > imin=5,
> > gbsa=1,
>
> PBSA calculates the non-polar energies on its own, so there is no need to
> set gbsa=1 here.
>
> What is happening is the surface area is being calculated twice.
>
> I would suggest looking through the pbsa section of the manual for details
> about available pbsa parameters (or using MMPBSA.py to create a sample
> input file.
>
> > surften=1,
>
> This sets the surface tension to 1. Therefore, the esurf and enpolar will
> be the LCPO-calculated SASA, to which you have to multiply your real
> surface tension (e.g., 0.0072 is used for MMPBSA.py calculations in GB
> solvent) in order to get non-polar energies.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Apr 10 2012 - 10:30:04 PDT
