AMBER Archive (2004)

Subject: AMBER: some questions....

From: Germán Sciaini (
Date: Wed Dec 08 2004 - 10:49:55 CST

Hi amber users,

I am trying to build a rigid molecule of ammonia, the molecule have four
sites, 3 charges q on the hydrogen atoms, a Lennard Jones´ potential on the
nitrogen atom and one extra point with a charge of -3q close to the N.
My first problem is the extra point doesn´t work like extra-point. And the
second is that when I am trying to link all atom together in order of doing
shake upon all bonds....the program say coordination number´s exceed...

If someone know what I have to change to extra point works out and how to
do rigid this molecule I´ll be very grateful.

Thanks in advance.


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