Print

Print


Hi David,

Thanks for answering my question. The extra character threw me off and I 
couldn't find the residue in the prep files. I know there's a Glycam 
Naming page (http://glycam.org/docs/forcefield/glycam-naming-2/) which I 
refer to regularly. Could the fourth character information be put on 
that page? I know it now but I think it'd be helpful for others. Of 
course if it's already somewhere else please let me know.

Thanks,

Laura

On 12/19/2017 12:35 PM, David Thieker wrote:
> The fourth character is simply a placeholder that differentiates the 
> ring conformations that are built. There are currently three that are 
> used (4uA1/4uA2/4uA3) that build the 1C4, 2So, and 4C1 conformations 
> (not necessarily in that order). This is currently only performed for 
> IdoA due to the flexibility of the ring compared to other 
> monosaccharides.
>
> Note that tLeap ignores the fourth character when reading PDB files.
>
> Best,
> David
>
> On Tue, Dec 19, 2017 at 11:48 AM, Laura Morris <[log in to unmask] 
> <mailto:[log in to unmask]>> wrote:
>
>     Recently I've gotten a PDB file from glycam.org
>     <http://glycam.org> that contains residues 4uA1 and 0uA1.
>
>     Why is there a 1 in the residue designation and are these really
>     4uA and 0uA?
>
>     -- 
>     Laura C. Morris
>     Scientific Computing Professional
>     Prestegard & Edison Labs
>     Complex Carbohydrate Research Center
>     [log in to unmask] <mailto:[log in to unmask]>
>     706-542-0305 <tel:706-542-0305>
>
>
>     ---
>     This email has been checked for viruses by Avast antivirus software.
>     https://www.avast.com/antivirus <https://www.avast.com/antivirus>
>
>
>
>
> -- 
> David F. Thieker, Ph.D.
> Biochemistry and Molecular Biology
> Complex Carbohydrate Research Center
> University of Georgia, Athens, GA
>
>

-- 
Laura C. Morris
Scientific Computing Professional
Prestegard & Edison Labs
Complex Carbohydrate Research Center
[log in to unmask]
706-542-0305