First off: Are your sugars in order from reducing end to non-reducing end?
If so: Yay, your life is easier.
If not: You will need to place TER cards between each residue then
connect them using bond commands in the tleap input file.
Next: Is there a hydroxyl group attached to the reducing end sugar?
If so, just make sure the O (and H if present) are separated into
another residue with a unique number. Name the residue ROH and name
the O as "O1" and the H as "HO1". Take care to preserve the PDB
columns.
Finally: If your sugar is branched, place TER cards after each branch
point and then at the end of each chain. Then, re-connect using bond
commands in tleap.
On Wed, Sep 5, 2012 at 3:44 PM, Pedro Swagger <pedrito.swagger.gmail.com> wrote:
> Dear all,
>
> I want to add ROH to an oligosaccharide that is not attached to any part of
> a protein. However I dont know how to do it. I try the following but it
> adds the ROH but very far from the oligosaccharide, Could you please help
> me?
>
> my oligosaccharide is store in a pdb but it does not have ROH.
>
> Thanks for your help
>
> ####################################
> source leaprc.ff03.r1
> source leaprc.GLYCAM_06h
>
>
> X = loadpdb glycam.pdb
>
> N = sequence { ROH X }
>
> savepdb N new.pdb
>
>
>
> --
> Pedro
>
> Saludos
>
> Departamento de Física,
> Facultad de Ciencias,
>
> Universidad de Chile
> Las Palmeras 3425, Ñuñoa, Santiago, Chile
> _______________________________________________
> 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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Received on Wed Sep 05 2012 - 13:00:10 PDT
