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----
tleap -s -f leaprc.GLYCAM_06
com = loadpdb lig.pdb
bond com.1.O1 com.2.C1
bond com.2.O3 com.3.C1
bond com.2.O6 com.4.C1
saveamberparm com lig_tmp.top lig_tmp.crd
savepdb com lig_tmp.pdb
----
I then used top2mol2 command to create lig_tmp.mol2 file from top and crd
files.
The structure I am getting looks good, however, I yet to run the MD.
I will be very thankful if you can cross-check this procedure.
Manoj
On Mon, Sep 6, 2010 at 12:24 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> 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
> >
> > _______________________________________________
> > 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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>