AMBER Archive (2006)

Subject: Re: AMBER: CARNAL: H-BOND Specifying side chains only

From: Bill Ross (
Date: Tue Feb 21 2006 - 15:41:25 CST

> I would like to know how you specify just the side chain under h-bond in
> carnal.

There is no simple way to do this that I (the author) can recall.

I forget whether the GROUP definition can include 'chain types',
but if so, specifying the negation of the group w/ chain type M
would get all the atoms that are not part of the backbone,
however this would include atoms like phosphate O's.

In any case carnal will be dropped from a future (next?) release
of amber (possibly unless someone wants to maintain it); probably
it is better to re-ask this question about ptraj. However no
matter what analysis program is used, I think some topological
analysis code might need to be written.

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