AMBER Archive (2009)

Subject: Re: [AMBER] Watercap... some querries

From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Date: Wed Jan 28 2009 - 09:10:48 CST

Thanks a lot dac...

________________________________
From: David A. Case <case_at_biomaps.rutgers.edu>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Wednesday, January 28, 2009 5:01:46 PM
Subject: Re: [AMBER] Watercap... some querries

On Wed, Jan 28, 2009, Waqas Nasir wrote:
>
> Well, just wanted to
> ask if I use multiple "solvatecap" commands for the explicit solvent,
> will it have any negative effect on the simulation... I mean does the "overall"
> cap need to be spherical always or we can use multiple solvatecap
> commands to cover irregular portions of the system and hence generate
> an overall irregular shaped water covered area. Or may be using a
> larger cap with the center deeper into the protein is recommended?

I don't think sander/pmemd support multiple caps ... there is just one.

>
> Moreover,
> when igb=10 with watercap enabled, does that mean that the atoms
> outside the cap are in the implicit solvent simulation

Yes.

...dac

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