Re: AMBER: Sander

From: David A. Case <>
Date: Mon, 9 Aug 2004 15:21:12 -0700

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

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Received on Mon Aug 09 2004 - 23:53:01 PDT
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