sir,
then could i extract "solvent exposed surface area of those residues"
from the trajectory data
thanking you
mary
On 11/27/14, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Nov 25, 2014 at 2:59 AM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
>
>> Sir,
>> is there any way to quantify or qualify the hydrophobicity of
>> nucleobases involved in stacking in amber.?
>>
>
> There is no "hydrophobic"
>
> part of the potential energy function in any of the "typical" force
> fields (e.g., Amber, CHARMM, GROMOS, ... etc.) -- it is a side-effect of
> the nonbonded interactions (electrostatic and van der Waals). Quantifying
> it would require an actual formula that defines it, and I'm not familiar
> with any such formula.
>
> As far as getting a qualitative measure -- it seems to me that
> hydrophobicity would correlate (probably strongly?) with the solvent
> exposed surface area of those residues, so I would probably use that
> relationship in order to compare "hydrophobicities" of different residues.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 26 2014 - 22:30:02 PST
