Thanks but what I want is to add th ROH. My sugars are placed in order from
reducing end. But there is no ROH in the pdb. I was asking for some command
to add the ROH and that it is near the reducing end. I can add ROH but it
is very far from the reducing end.
Can you help me to do that?
Thanks so much
On Wed, Sep 5, 2012 at 3:58 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Pedro
Saludos
Departamento de Física,
Facultad de Ciencias,
Universidad de Chile
Las Palmeras 3425, Ñuñoa, Santiago, Chile
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Received on Wed Sep 05 2012 - 13:30:04 PDT
