Yes here is my PDB.
Thanks so much
On Wed, Sep 5, 2012 at 4:30 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> Can you send me your pdb?
>
> On Wed, Sep 5, 2012 at 4:28 PM, Pedro Swagger <pedrito.swagger.gmail.com>
> wrote:
> > 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
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > 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
> AMBER.ambermd.org
> 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 - 14:00:04 PDT
