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 - 12:30:03 PDT
