Last question, the ROH group is not connected to my sugars right? Do I need
to add a bond connection command in tleap to make sure, they will be bound?
or It is NOT necesary.
Thanks
On Thu, Sep 6, 2012 at 12:44 PM, Pedro Swagger <pedrito.swagger.gmail.com>wrote:
> 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
>
--
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
