AMBER Archive (2009)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Jan 28 2009 - 12:46:02 CST

Through release 10, pmemd does not support watercaps in any form.
Regards - Bob Duke

----- Original Message -----
From: "David A. Case" <case_at_biomaps.rutgers.edu>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Wednesday, January 28, 2009 10:01 AM
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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