The structure in the pdb file you attached is:
a-D-Manp-(1-3)-[a-D-Manp-(1-6)]-a-D-Manp-(1-)-OH
In other words, a single alpha D mannopyranose has two others attached
at its 3 and 6 positions. If that is what you want, and I think
perhaps it is, then the structure is correct.
To read the pdb into leap, you will need to place TER cards (in the
pdb file) between each of your residues then manually link them back
together in the proper order using the bond command within leap. When
a residue (your first one, VMA), is attached to more than one other
residue, leap is not always able to identify the attachment points for
subsequent residues. Inspection using VMD tells me that residue 2 is
attached at the three position and residue 3, at 6. You should also
terminate at the end of each chain (e.g., the 0MA), because if not,
you are essentially telling leap to bond that residue to the next one,
which is not what you want. Leap will happily do whatever you tell it
to do without regard to chemical sense (this is a good thing, but one
must respect it).
There are further instructions for building a glycoprotein in the
AmberTools manual. The online glycoprotein builder should be
functional again in a day or two.
:-) Lachele
On Mon, Sep 6, 2010 at 12:05 PM, manoj singh <mks.amber.gmail.com> wrote:
> Hi,
>
> I want to simulate a protein-carbohydrate system using ff99SB and GLYCAM in
> Amber10. I am little confused over various issues with GLYCAM. First is the
> residue nomenclature.
> I want to simulate {alphaMAN-1-->6-alphaMAN-3-->1-alphaMAN}. The structure
> of the ligand is attached with the mail. Attached is the PDB file with
> residue name, which I think is consistent with the GLYCAM. I will be very
> thankful if someone can verify this.
>
> Manoj
>
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>
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Sep 06 2010 - 09:30:04 PDT
