Dear Amber Users,
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"
Now the production run is almost over.Do you suggest me to change my
intiial files with a valid value for "PN" If so also let me know how can I
obtain this.
Thanks
Kirtana
On Tue, Jun 12, 2012 at 3:59 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, Jun 12, 2012 at 1:50 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Tue, Jun 12, 2012, kirtana S wrote:
> >
> > > Is there any way I can obtain the entropy in free and bound states .
> >
> > The most common approach is to compute normal modes, which can be useful
> if
> > your free and bound states have well-defined native structures. The
> > floppier
> > the molecule, the less useful this approximation is.
> >
> > Note that the entropy of the "bound" state (probably) has to include the
> > ligand. You have to be at a local minimum in the energy, so you can't
> just
> > remove the ligand and somehow obtain an estimate of the entropy.
> >
> > There are other ways of estimating configurational entropies, but all of
> > this
> > depends a lot on what sort of system you have, and I don't think(?) you
> > have
> > said things much more specific that it being a "single polymer chain".
> >
> > ....dac
> >
> > p.s.: if you try the normal mode route, I strongly recommend using the
> > nmode() function in NAB, not the standalone "nmode" program.
> >
>
> As a note of caution here. The reason that MMPBSA.py complained about a
> 'bad periodicity' is because it was using a NAB program to calculate the
> normal modes. As Dave already pointed out, this is worrisome, and needs to
> be fixed before you can use normal mode analysis. sander and pmemd use a
> different algorithm to calculate the dihedral energy, which is why it did
> not complain about the bad periodicity. However, both nmode and NAB's
> nmode function use the method that fails when periodicity != (1,2,3,4,5,6).
>
> Allowed periodicity values (when your phase shift is either 0 or 180
> degrees) are 1 through 6, inclusive. My guess is that one of your dihedral
> parameters has a periodicity of "0", which would need to be checked out
> (you can use xparmed.py or parmed.py to look into this). You can delete
> this dihedral with xparmed.py (or parmed.py) if you want, and then your
> calculation should stop crashing -- this still has to be validated, though.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Jun 13 2012 - 10:00:03 PDT
