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
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Fri Oct 05 2012 - 00:30:02 PDT
