Is there any way I can obtain the entropy in free and bound states .
Thanks
Kirtana
On Mon, Jun 11, 2012 at 9:48 PM, case <case.biomaps.rutgers.edu> wrote:
> On Mon, Jun 11, 2012, kirtana S wrote:
>
> > I am using mm_pbsa.pl to calculate entropy of a single polymer chain and
> > then entropy of the complex.
> > When I calculate the entropy of single polymer chain using mm_pbsa.pl ,
> I
> > need to specify ligand and receptor , how can i work with this .
>
> Let me quote from the introduction to mmpbsa (from the AmberTools12
> Reference
> Manual):
>
> "None of these should be considered as a “black-box”, and users
> should be familiar with Amber before attempting these sorts of
> calculations. These scripts automate a series of calculations, and cannot
> trap all the types of errors that might occur. You should be sure that you
> know how to carry out an MM-PBSA calculation “by hand” (i.e., without
> using the scripts); if you don’t understand in detail what is going on,
> you will have no good reason to trust the results. "
>
> Basically, I'm arguing that you are asking the wrong question: you can
> look at
> the scripts to see what mm_pbsa.pl does, but you really need to
> understand how
> mmpbsa calculates entropies (of anything) before attempting to use the
> scripts.
>
> That said, the "ligand" is the item you add to the "receptor" (generally a
> protein chain) to get the "complex". It's not clear what your "polymer
> chain"
> is here, but if it is something without a well-defined native structure,
> the
> mmpbsa scripts will not produce a useful estimate of its configurational
> entropy.
>
> > I am not able to use MMPBSA.py as this detects an invalid periodicity in
> my
> > force field paramters.
>
> This sounds dangerous: the fact that an older script might not have as
> much error checking as more recent ones is not a good reason to carry out
> calculations where the prmtop file has invalid torsional parameters. You
> need to track down the origin of this problem.
>
> ....dac
>
>
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Received on Tue Jun 12 2012 - 09:30:04 PDT
