AMBER Archive (2003)

Subject: Re: AMBER question

From: David A. Case (case_at_scripps.edu)
Date: Fri Jun 20 2003 - 19:59:04 CDT

On Sat, Jun 21, 2003, David wrote:
>
>
> 1.How to tell the difference between sp2 carbon atom and sp3 carbon atom
> when carbon atom is the central atom in torsion angle?

I don't understand the question...although LEaP sometimes prints out warnings
if there sp2 atoms without torsions, fundamentally it doesn't care about this.
It just uses the atom types to match up torsions with parameters.

>
> 2.Does AMBER have the rule that determines the atom-correspondence while
> determining the torsion?
>

See above. If this is not what you are asking, you will need to ask a more
detailed question: what particular problem are you trying to solve?

.regards...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================