Thanks Lachele.
By changing the glycosylation site to a non-terminal amino acid, I produced
the topology file successfully.
JH
On Sat, Jan 15, 2011 at 9:44 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> 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
> (http://glycam.ccrc.uga.edu/ccrc/pages/temp/gl_params.jsp). 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
> leap.
>
> * 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 (glycam.org/ccrc/gp) 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
> manual?
>
> :-) Lachele
>
>
> On Sat, Jan 15, 2011 at 10:20 PM, Jianhui Tian <jianhuitian.gmail.com>
> 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Jan 16 2011 - 09:30:04 PST
