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GLYCAM-L  March 2020

GLYCAM-L March 2020

Subject:

Re: Reg: Protonated Glucosamine residues

From:

Lachele Foley <[log in to unmask]>

Reply-To:

Users of GLYCAM & GLYCAM-Web <[log in to unmask]>

Date:

Fri, 27 Mar 2020 01:49:23 -0400

Content-Type:

text/plain

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Parts/Attachments

text/plain (25 lines)

Sorry no one has responded yet.  We're all really preoccupied right
now.  I'll try to get to this on the weekend if someone else doesn't
before.

On Tue, Mar 24, 2020 at 10:46 AM Lara rajam <[log in to unmask]> wrote:
>
> Dear Glycam,
>  I am interested in looking into Glucosamine parameter for NH2 and protonated residues.
> I have downloaded the prep files from GLYCAM. Thanks for the wonderful work.
> When I loaded them in the Xleap I saw that the O4 is with H(H4O) hydrogen and has a charge 0.4450. I am not aware how to link this to another acid residue. since the issue of the charge is not making integer charge.
>
> When I looked into other sequences the glycosidic oxygen O4 has a constant charge -0.5080.
> but in the NH2  parameters they are -0.7160. If I make these in a middle of a sequecne how to fix this issue, Also noticed that the residue type labeling is only one for the amine 0YN for alpha and 0Yn for beta not like GlcNS6S residues of different possible linkage types.
>
> - Please advise me how to fix this for NH2 and NH3+ residues?
>
> - Thank you



-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA

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