I believe you might be the first person to try N-linking a sugar with
an attachment at the 2-position. We are discussing the most
appropriate resolution. I will respond as soon as I can.
On Thu, Sep 12, 2013 at 1:31 PM, lara lara <lara.4884.gmail.com> wrote:
> dear amber !
>
> I am trying to fuse the protein to the glycans in xleap using the GLYCAM_06
> lib.
>
> When I went through the documentation the N -glycosylation site for ASN
> residue must be changed to label NLN , I did it.
>
> I tried to build the carbohydrate from the side chain of the ASN , in the
> atom ND2 , I am able to build it , but when I saved the parameter file It
> says the error in Building topology.
>
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> ** No torsion terms for Os-Cg-Cg-N
> Building improper torsion parameters.
> old PREP-specified impropers:
> total 364 improper torsions applied
> 0 improper torsions in old prep form
> Building H-Bond parameters.
> Parameter file was not saved.
>
> I feel that the atom type to the atoms should be changed , but i dont know
> which type is relevant ( the ND2 type is N so that is saying error )
>
> how to fix this ?
>
> thanks in advance
> _______________________________________________
> 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
Received on Thu Sep 12 2013 - 11:30:27 PDT
