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://amber.ch.ic.ac.uk/Questions/mail/100.html
..hope this helps...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Tue Jan 14 2003 - 14:29:43 PST
