Sure, thanks. I will try that also. Is it safe to cover the existing file
with the updated libraries?
JH
On Sun, Jan 16, 2011 at 10:38 AM, Lachele Foley (Lists)
<lf.list.gmail.com>wrote:
> You can glycosylate a terminal amino acid if that is what you want to
> do, but you will need the updated libraries. We didn't make a bugfix
> for that because people very seldom want to do that.
>
>
> On Sun, Jan 16, 2011 at 12:22 PM, Jianhui Tian <jianhuitian.gmail.com>
> wrote:
> > 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jan 16 2011 - 10:00:06 PST
