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
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Received on Thu Sep 06 2012 - 09:30:05 PDT
