AMBER Archive (2004)

Subject: Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function

From: David A. Case (case_at_scripps.edu)
Date: Thu Feb 12 2004 - 10:41:16 CST


On Thu, Feb 12, 2004, Ma?gorzata Jaro?czyk wrote:

> I use Amber v. 7.0, and I found in manual that I should use commands:
> dielc=4, idiel=0,

Did you really see this in the manual? "idiel" is no longer a variable
in the sander of Amber 7. (I did a quick search in the sander section
of the Amber Manual, and could not find this....)

> but should I use also in the input line the command
> eedmeth=5
> to have distance dependent dielectric function?

Yes, you need to set eedmeth=5 to get a distance dependent dielectric.

...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