[AMBER] How to get the information of hydrophobic contact?

From: qiao xue <xueqiaoup.gmail.com>
Date: Thu, 8 Mar 2012 11:03:48 +0800

Hello all,

I read a paper which use AMBER MD simulations. Their analysis contain
the hydrophobic contacts. They define the hydrophobic contact for a
pair of the hydrophobic side chains of residues(Ala, Cys, Phe, Leu,
Met, Ile, Val) was considered to be formed when a minimal distance
between the center of mass of any pair of residues is less than 5.4A.

I read the Ambertools help and find a command "contacts". But it seems
that it could not do the analysis above. So would I ask a question
that how to do this analysis?

The other question is that if I want to constrain the residues with
mask. e.g. I just want to know the interaction among Ala, Cys, Phe.
Can I write like this: :Ala, Cys, Phe.CA?


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Received on Wed Mar 07 2012 - 19:30:02 PST
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