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 Tue Jun 12 2012 - 13:30:02 PDT
