We don't have a parameter that has been validated for that linkage.
But, there is something you can use. It should work reasonably well,
but if you can find some way to validate it, that would be ideal.
The suggestion is to use the Os-Cg-Cg-Ng term for Os-Cg-Cg-N. This is
analogous to the treatment for Oh-Cg-Cg-Ng and Oh-Cg-Cg-N, so it has
precedent.
If you want to do that, just copy the "Os-Cg-Cg-Ng" line from the
parameter file to a new line that starts with "Oh-Cg-Cg-N ". Note the
space after N to ensure that the alignment is preserved.
On Thu, Sep 12, 2013 at 2:10 PM, Lachele Foley <lf.list.gmail.com> wrote:
> 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
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Sep 12 2013 - 15:00:02 PDT
