AMBER Archive (2003)

Subject: Re: AMBER: Gibbs pmf calculation

From: David A. Case (case_at_scripps.edu)
Date: Fri Aug 15 2003 - 11:51:07 CDT

On Fri, Aug 15, 2003, Lishan Yao wrote:

> I want to use Gibbs PMF method (umbrella sampling) to pull out the
> ligand from active site to calculate binding free energy. I need a
> distance restraint. But when I look at the Manual, I find out nmropt
> belongs to sander. What should I do?

Please see pp. 184-188 and 191-192 of the Users' Manual.

..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
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu