Re: [AMBER] Parameter missing in Glycan

From: Lachele Foley (Lists) <"Lachele>
Date: Sat, 15 Jan 2011 23:44:15 -0500

The way to fix it depends on your situation. The problem is that you
have instructed leap to bond atoms together for which it does not have
sufficient rules. Here are a few guesses.

* If you are loading a pdb file and there is not a TER card between
the last amino acid and the first glycan residue, then you need one.
You will have to set the bonding between glycan and protein explicitly
within leap. The AmberTools manual contains more information.

* If you are trying to attach the glycan to a terminal amino acid,
then you need to download fresh library files from our site
( Just copy
those over the existing ones in your amber tree or specify their path
in a customized leap input file.

* It is possible that the amino acid to which the glycan attaches was
not renamed properly.

* You might be asking leap to bond the glycan to the PDB residue
number, which might not be the same number assigned internally by

* It is also possible that the residue(s) in your glycan are not named
properly, are in the wrong order, etc.

If none of those is the problem, or if you still need help, then I
need more info. Did you use our builder ( to
generate a pdb to use for input? If not, how did you build the
glycoprotein? What were the specific commands you issued to leap?
Which version of Amber? If the Amber is recent enough, which version
of AmberTools? Did you follow the instructions in the AmberTools

:-) Lachele

On Sat, Jan 15, 2011 at 10:20 PM, Jianhui Tian <> wrote:
> Hi,
> I am trying to build the topology for a glycoprotein in Xleap using
> Glycam_06 and AMBER99SB. When I try to save the topology, it gives warning
> that:
> Could not find angle parameter: N - CT - HP
> Can anyone tell me how to solve the problem? Thanks a lot.
> JH
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Sat Jan 15 2011 - 21:00:02 PST
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