AMBER Archive (2004)

Subject: Re: AMBER: Sander

From: David A. Case (
Date: Mon Aug 09 2004 - 17:21:12 CDT

On Mon, Aug 09, 2004, sachin patil wrote:

> So, for a cap size of 1342 atoms what restrain
> potential I shall use so that the water molecules dont
> evaporate?

If you used the "solvatecap" option in leap to make the cap, you already
have a center and a radius from that. You just need to set a non-zero value
for "fcap" in sander. If you built the cap by some other method, you will
have to figure out good values for all of the cap-related parameters.

...good luck....dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to