Thanks! Glad you like them! We'll start rolling out an improved
version of the site very soon. :-)
On Sun, Dec 16, 2012 at 1:54 AM, Aron Broom <broomsday.gmail.com> wrote:
> As a totally random aside, thank you for providing the facilities you do.
> I work with oligosaccharides, and your group's website is valuable.
>
> ~Aron
>
> On Sat, Dec 15, 2012 at 10:01 PM, Lachele Foley (Lists)
> <lf.list.gmail.com>wrote:
>
>> We don't have structural and charge information for muramic acid. I'm
>> not aware that anyone in the group is working on it either. Our
>> parameters should work, but you would need to develop charges.
>>
>>
>> On Sat, Dec 15, 2012 at 5:16 PM, Aron Broom <broomsday.gmail.com> wrote:
>> > Have you considered using the Glycan builder by the group that makes the
>> > AMBER Glycam forcefield (Woods group)?
>> >
>> > You can find their main website here http://glycam.ccrc.uga.edu/ccrc/
>> >
>> > Follow the amber utilities or somesuch and then carbohydrate builder or
>> > something. This will allow you to not only generate a PDB easily, but
>> all
>> > the residues will have the appropriate names.
>> >
>> > ~Aron
>> >
>> > On Sat, Dec 15, 2012 at 3:25 PM, Krisztina Feher
>> > <feher_krisztina.yahoo.com>wrote:
>> >
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Dear All,
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> I am trying to generate a disaccharide consisting
>> >> bGlcpNAc[1,4]aGlcpNAc[3-]-lactic acid in leap, see in the attched pdb
>> file.
>> >> Could someone suggest me the monosaccharide units I should use for
>> >> this molecule? My own attempt from 4 residues ROH 1, WYB 2, 1YB 3 and
>> >> a self-constructed LAC 4 residue has incorrect connections, please, see
>> >> the screenshot of molecule in the editor.
>> >>
>> >> GlcpNAc[3-]-lactic acid is in fact muramic
>> >> acid, but I did not see separate PDB code for in the GLYCMA06.prep
>> >> file, so I made it from GlcpNAc and a lib file for lactic acid in
>> >> antechamber with gaff atomtypes. Is there a better way for muramic acid?
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Thanks in advance,
>> >>
>> >> Krisztina
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> >
>> >
>> > --
>> > Aron Broom M.Sc
>> > PhD Student
>> > Department of Chemistry
>> > University of Waterloo
>> > _______________________________________________
>> > 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
>>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
> 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 Sun Dec 16 2012 - 10:30:02 PST
