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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

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




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

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Lachele Foley
CCRC/UGA
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