Thanks so much, You are right, I took it from a larger molecule. I put
everything together and the charge is now zero.
Thanks so much, I appreciate it.
On Thu, Sep 6, 2012 at 12:18 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> The final residue in your sequence, VMA, is designed to have
> additional components attached to it at positions 3 and 6. I suspect
> you extracted this sequence from a larger, branched oligosaccharide.
> That's fine, but you need to either add two things to the VMA or
> change its name. If you intended that to be the final residue in your
> sequence, you can simply change the name from VMA to 0MA (that's a
> zero, not a capital O). If you do that, tleap will add the missing
> hydrogens and the charge will be correct.
>
> To see our naming convention:
> http://glycam.ccrc.uga.edu/ccrc/pages/cncg.html
>
>
> On Thu, Sep 6, 2012 at 11:49 AM, Pedro Swagger
> <pedrito.swagger.gmail.com> wrote:
> > 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
> > _______________________________________________
> > 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 - 10:00:04 PDT
