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
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat Dec 15 2012 - 19:30:02 PST
