From chemistry-request $#at#$ server.ccl.net Mon Aug 20 12:10:39 2001
Received: from phm.utoronto.ca ([128.100.70.1])
	by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7KGAdM19453
	for <chemistry -8 at 8- ccl.net>; Mon, 20 Aug 2001 12:10:39 -0400
Received: from phm.utoronto.ca (lpk04.phm.utoronto.ca [128.100.70.180])
	by phm.utoronto.ca (8.9.3+Sun/8.9.3) with ESMTP id MAA08648
	for <chemistry -x- at -x- ccl.net>; Mon, 20 Aug 2001 12:05:07 -0400 (EDT)
Sender: william:~at~:phm.utoronto.ca
Message-ID: <3B81362B.BAE4B2D -8 at 8- phm.utoronto.ca>
Date: Mon, 20 Aug 2001 12:09:15 -0400
From: William Wei <william -x- at -x- phm.utoronto.ca>
Reply-To: william(+ at +)phm.utoronto.ca
Organization: Faculty of Pharmacy, U of T
X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30)
X-Accept-Language: en
MIME-Version: 1.0
To: chemistry&$at$&ccl.net
Subject: About amber parameters
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi, Dear CCL'ers,

I am a new user of amber. I have problems with developing parameters.
Here is my steps:

1.  Create new residue, import two residues from amber, connect them,
and draw other part of the new residue.
2.  Save the new residue in PDB file. Open it with sybyl, and the bonds
I drawn between residues(amber) were lost.  I drew it, and use mopac to
caculate the charge.
3.  Construct the charge, atoms type in xleap.
4.  Construct the force parameters for the new residues.
After these steps, I load the new residue OFF file and new force
parameters, check the unit, it is okay. Then my problem was coming:
while I ran xleap, load my new residue,  xleap can not recognize my new
atoms tpye.  And while I save the residue to pdb file in leap, The sybyl
can not draw it well.  Does anyone have developed parameters? I really
appreciate your help. Or give me some information of amber .OFF file's
type.

William.