Yes ... PBSA has been mostly used in calculations with radii from the
prmtop files ...
And, you can change sprob to play with the effect of the solvent probe
radius on the surface area.
All the best,
Ray
On Mon, Sep 12, 2011 at 7:01 PM, kirtana S <skirtana4.gmail.com> wrote:
> 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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>>
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Received on Tue Sep 13 2011 - 12:00:04 PDT
