Subject: summary : Amber calculations

From: Belletete Michel <[email-masked]>
Date: Tue, 2 May 1995 12:36:34 -0400 (EDT)

Thanks to everyone who responded to my mail "amber calculations" dated 
April 25. I am summarising the responses below:

The problem that I have been facing is the lack of bending parameters for 
atom types OS-CT-OS for AMBER calculations using Hyperchem.

    The origin of the problem is that I used Model builder of Hyperchem 
to build my molecule. This builder does not recognise the anomeric effect 
in carbohydrates. Homan in his paper Biochemistry: 29,9110(1990) defines 
additional atom types for the ring 0xygen and for both C1 and O1 in alpha 
and beta sugars. This is needed to account for the distinctly different 
bond lengths and angles about C1 in sugars.

     The solution is to buy Chem plus and use the saccharide builder and 
the problem of OS-CT-OS atom types will disappear.If you have edition 4 
of Hyperchem but not chem plus, then compile the AmberS.. .txt. In you 
*.hin files, change the atom types of ring oxygen to OE instead of OS and 
the atom types C1 to AC if it is an alpha sugar and BC if beta sugar. 
Minimization should proceed smoothly. 

     The crux of the problem thus was the wrong atom types defined in my 
molecule. The AMBER calculations does not work with these atom types. 

     I hope this summarises the answers to the problem.

 Michel