From: Yulian Gavrilov <zzeppelin87.gmail.com>
Date: Tue, 10 Nov 2015 10:24:42 +0200

Dear all,

I have a question about GIST.

In the tutorial and manual it is written that the protein should be rigid
in order to use GIST to analyze water around it.

Is there any way to analyze hydration water around a flexible molecule?
I would like to compare the thermodynamic parameters (dA, dTS, dE) of
hydration water around the flexible and rigid version of a peptide. Is
there any way to do it?
I use AmberTools15.

Only idea that I have is to devide the output trajectory of the flexible
peptide into several clusters based on RMSD, so that within the cluster the
flexibility of a peptide will be minimal. Then I can use GIST for each
cluster separately. But this way I won't get the right entropy values,

Thank you in advance for any ideas!

Yulian Gavrilov
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Received on Tue Nov 10 2015 - 00:30:03 PST
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