AMBER Archive (2004)

Subject: Re: AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 08 2004 - 18:15:12 CST


On Thu, Jan 08, 2004, Anna Schrey wrote:
> dear AMBER community,
>
> I am trying to minimize a protein containing a - manually parametrized -
> small-molecule ligand. This is my sander input file
>
> cut=8.0,

You need to set cut to a large value (say 999.) in order to get reliable
minimizations.

> ntmin=0, ncyc=10, ntb=0,nmropt=y,

nmropt is an integer (0,1,2) not a letter

..good luck...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