On Wed, Jun 13, 2012, kirtana S wrote:
>
> I want to calculate the change in entropy of a polymer chain when this
> binds to a modified fullerene.
> The dihedral periodicity is associated with the fullerene. The periodicity
> of one dihedral is 0 with phase angle 0 at the connectivity with the
> modified functional group. In the AMBER file formats this says "If PN .lt.
> 0.0 then the torsional potential
> is assumed to have more than one term"
Where did these torsion potentials come from? Is there more than one term
for this particular torsion? Note that a torsion potential with
a periodicity of zero just adds a constant to the energy. That is probably
not what you want (or what whoever developed this fullerene force field
intended.) You need to track down what is supposed to be happening.
And, to repeat my earlier comment: I'm rather concerned about your continued
use of the term "polymer chain". I recognize that you may not wish to make
the nature of this entity public, but if it is the sort of (floppy) molecule
that is often described as a "polymer chain", the normal mode method
implemented in MM-PBSA will *not* provide any useful estimate of the change in
entropy upon binding to a fullerene.
....dac
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Received on Thu Jun 14 2012 - 05:30:02 PDT
