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 Mon Jun 11 2012 - 19:00:04 PDT
