AMBER Archive (2002)

Subject: Re: the tree name?

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 27 2002 - 16:44:17 CST

On Tue, Nov 26, 2002, Sichun Yang wrote:

> In the Group Specification of the manul,
> There is a parameter called the TREE NAME of the atom among a series of
> filter specifications.
> So what does the TREE NAME mean?

See http://www.amber.ucsf.edu/amber/doc/prep.html

But tree names are obsolete, and it is not guaranteed that they will
be correct in the prmtop file. I'd recommend not using them.

Tom Cheatham is coming up with a scheme that will allow a much simpler
definition of groups (isn't that right, Tom?? :-) ).

..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
==================================================================