Sorry I stated wrong it is Ambertools 1.5 .
So does this take the atom radii from my topology files.
Now If I want to know the solvent accessible surface area for different
probe radii I can change the sprobe in my input file.
Thank you all
On Mon, Sep 12, 2011 at 3:22 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Sep 12, 2011 at 2:42 PM, kirtana S <skirtana4.gmail.com> wrote:
>
> > Now again I tried with Amber tools 1.4 , pbsa
> > using my input script for default values mostly and though this runs to
> > give
> > my output, Here I have attached my .out file ,please see if you can
> access
> > it.
> >
>
> Why not AmberTools 1.5?
>
>
> >
> > I would like to know about
> > PB Info in pb_read(): npopt has been overwritten with inp
> >
>
> inp is the new npopt. In previous versions, npopt was the variable that
> specified the non-polar solvation free energy calculation method. In the
> future it is going to be inp. This is just a verbose warning about that.
>
>
> >
> >
> > How does this rectify to get the input for atom radius. Can you clarify
> me
> > to get the exact solvent accessible surface area for my molecule.
> >
> > As per manual I used sprob = 1.6 , which was the default value.Which
> ither
> > parameters I should take into consideration in my input , if I have some
> > atoms like Iron.
> >
>
> This is not the radius for any atom in your system. It is the probe radius
> used to calculate the solvent-accessible surface area (SASA).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Sep 12 2011 - 19:30:02 PDT
