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
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AMBER mailing list
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Received on Wed Sep 05 2012 - 14:00:03 PDT
