AMBER Archive (2003)

Subject: Re: solvatecap

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 14 2003 - 16:29:43 CST

On Tue, Jan 14, 2003, GUILLERMINA L ESTIU wrote:

> I am trying to run a MD calculation using the watercap option When I finally
> got everything to work, I have received an error message in the output that
> seems to indicate that I have to rebuild the crd and top files placing the
> moving atoms in the beginning. Is it possible?
>
> This is the message in the output
>
> LOADING THE BELLY ATOMS AS GROUPS
>
> ----- READING GROUP 1; TITLE:
> belly residuos que se mueven
> GRP 1 RES 800 TO 9411
> Number of atoms in this group = 35447
> ----- END OF GROUP READ -----
> When igb>0, the moving part must be at the
> start of the molecule. This does not seem
> to be the case here.
> natbel,i,igroup(i) = 35447 35448 1
>

In the first place, you should not be using generalized Born (implicit
solvent) in combination with a solvent cap (explicit solvent). You need
to choose one or the other. It sounds like you want to set igb=0, then
the belly can be whatever you want.

If you *are* interested in belly + GB, see:

   http://www.amber.ucsf.edu/amber/Questions/mail/100.html

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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