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I have added a section on alternate residue codes/names.  Please let me
know if it would be useful to say something more or something different.

http://glycam.org/docs/forcefield/glycam-naming-2/


On Wed, Dec 20, 2017 at 10:03 AM, Xiaocong Wang <[log in to unmask]> wrote:

> Hi Laura,
>
>
> These residues have the same prep file.  For example, 4uA1, 4uA2, and 4uA3
> use the same prep file, 4uA.   As David mentioned in the last email, the
> last character indicates different conformations, but still the same
> residue.
>
>
> Best regards,
>
>
> Xiao
>
>
> Xiaocong Wang
> Complex Carbohydrate Research Center
> The University of Georgia
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> ------------------------------
> *From:* Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on
> behalf of Laura Morris <[log in to unmask]>
> *Sent:* Wednesday, December 20, 2017 9:47:15 AM
> *To:* [log in to unmask]
> *Subject:* glycam naming page on website -> Re: 4uA1 & 0uA1 (what's the
> 1?)
>
> 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]> wrote:
>
> Recently I've gotten a PDB file from 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]
> 706-542-0305
>
>
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> --
> 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 [log in to unmask] <(706)%20542-0305>
>
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-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA