It should be connected. To verify, VMD is useful. Try "vmd m.parm7
m.rst7" and inspect bonding.
On Thu, Sep 6, 2012 at 12:48 PM, Pedro Swagger
<pedrito.swagger.gmail.com> wrote:
> 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
> _______________________________________________
> 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 - 10:00:05 PDT
