AMBER Archive (2003)

Subject: Re: Leap to prep

From: caldwell_at_heimdal.compchem.ucsf.edu
Date: Mon Mar 03 2003 - 17:03:25 CST

presuming your unit has been named "a":

set a.1 connect0 a.1.XX
set a.1 connect1 a.1.YY

where "a" is the unit, "1" is the reside and XX/YY are the
atoms that will connect to the previous/next residues (if
and when you build this residue into a chain). If your residue
is not going to be in a macromolecule, you can use any atom
in the residue for XX/YY.

jim

On Mon, 3 Mar 2003, Dominico J Vigil wrote:

>
> Hi, I am trying to build a cyclic-AMP molecuole in xLeap and save it in
> the older prep format. I use the command saveamberprep but it says I need
> to define connect0 and connect1 atoms in order to do this. does anyone
> know how to do this?
> Thank you,
> Dom Vigil
> 

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