I have replaced hydroxy at the anomeric position to Sulfate and able to adjust the charges. I have difficulty with the residue name. My first sugar is PGB (PDB file is attached for your perusal). Glycam06j_1 doesn't include O1 in the PGB residue. How should I name the residue consisting of oxygen "O1" that is linked to PGB?
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We haven't tested phosphate charges explicitly, that's why we haven't released charges for phosphate on our webtool.
From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Neha S. Gandhi <[log in to unmask]>
Sent: Tuesday, June 12, 2018 8:41:36 PM
To: [log in to unmask]
Subject: Re: ADD PHOSPHATE DERIVATIVE
Mohit works with me, and he is acquainted using tleap in AMBER.
If I remember the charge correctly on anomeric position (OH) is -0.194. If we add sulphate at this position, how are the charges taken into account at the anomeric position?
GLYCAM has parameters for phosphate but not the charges.
Just to be sure I understand: You want to sulfate the monosaccharide at all positions including the anomeric position? You can't do that with the builder, but it can be done using tleap. Are you familiar with tleap?
I don't recall the status of the phosphate derivative development, but it isn't ready. Anyone know the status?
On Tue, Jun 12, 2018 at 10:14 AM, Mohit Chhabra <[log in to unmask]> wrote:
I have a 5-sugar units chain in my molecule and I want to substitute sulfate at all the positions but when I try to add sulfate as a derivative on the end terminal sugar, it always gives free OH at position 1 of sugar using "carbohydrate builder” option. If I download that file and add sulfate by replacing OH, the charge of sulfate will still be +0.194 as it was of OH but the charge of sulfate should be same as of other sulfates. If there is any possible way to design a fully sulfated carbohydrate, please suggest.
Also, I would like to add phosphate at the 6th position of mannose by replacing sulfate but couldn't add phosphate as derivative. There is an option to add phosphate as a derivative but it's not functioning. Please suggest what can be the possible way to do that or how the charges of phosphate can be derived.
Athens, GA USA