[AMBER] calculating intramolecular hydrogen bonding

From: Vijay Manickam Achari <vjrajamany.yahoo.com>
Date: Fri, 5 Oct 2012 08:29:22 +0100 (BST)

Dear Amber users,

Greetings to you.

I would like to calculate intramolecular hydrogen bonding for glycolipid (carbohydrate attached to alkyl chain via glycosidc linkage) such as octyl-glucopyranoside and octyl-galactopyranoside.

I remember there was carnal program which can do this in amber7 but now carnal is not shipped with amber9 onward. In this situation, how I could calculate intramolecular hydrogen bonding. 
I found one thread in amber mailing list talking about this (http://archive.ambermd.org/201007/0679.html) but I am not so clear how the "angle turning off" (angle = -1.0) could give intramolecular hydrogen bonding values.

Could anyone explain on this?
You kind help much appreciated.

Thank you.
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
AMBER mailing list
Received on Fri Oct 05 2012 - 00:30:02 PDT
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