Thank you so much. The second is working very well, it doesn't change
anything but add the ROH group.
Now I am wondering how to fixed the non integral charge. Could you please
tell me how to deal with that?
Thanks you for your great help.
On Wed, Sep 5, 2012 at 5:44 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> Heh... I'm not sure if you realize it, but you found one of tleap's
> more interesting features...
>
> Before we proceed: I assume you realize that your non-reducing end is
> also missing some bits. So, I'm not addressing that. It's the reason
> for this error:
>
> ERROR: The unperturbed charge of the unit: -0.388000 is not integral.
>
> If you need help with that, say so.
>
> The following is the way one would immediately think to do it. But,
> don't do this because tleap flips the chirality at the reducing end.
>
> ==========================
> "normal" way
> flips chirality (*)
> don't use!!
> ==========================
> source leaprc.GLYCAM_06h
> m = loadpdb new.pdb
> set m head m.164.C1
> m = sequence { ROH m }
> saveamberparm m flipped.parm7 flipped.rst7
> ==========================
>
> The following way is a workaround for the chirality flip. Depending
> on how you fill in the non-reducing end, this might require a few
> extra steps on your part.
>
> ==========================
> chirality maintaining workaround
> ==========================
> source leaprc.GLYCAM_06h
> m = loadpdb new.pdb
> n = copy ROH ## for safety in case you use ROH later in the session
> set m tail m.164.C1
> set n head n.1.O1
> m = sequence { m n }
> saveamberparm m m.parm7 m.rst7
> ==========================
>
> And... carefully inspect your files using something along the lines of:
>
> vmd m.parm7 m.rst7
>
> (*) During some operations, leap flips chirality at open-valence
> reducing-ends.
>
> :-) Lachele
>
>
> On Wed, Sep 5, 2012 at 4:36 PM, Pedro Swagger <pedrito.swagger.gmail.com>
> wrote:
> > 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
> >
> > _______________________________________________
> > 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 Thu Sep 06 2012 - 09:00:03 PDT
