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Which residue are you starting with?

If you haven't seen these instructions, they might help:

http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/



On Tue, Jun 12, 2018 at 9:48 PM, Xiaocong Wang <[log in to unmask]> wrote:

> Hi Neha,
>
> We haven't tested phosphate charges explicitly, that's why we haven't
> released charges for phosphate on our webtool.
>
> Best,
>
> Xiao
>
>
> Xiaocong Wang
> Complex Carbohydrate Research Center
> The University of Georgia
> <https://maps.google.com/?q=Georgia+%0D%0A+315+Riverbend+Road,+%0D%0A+Athens,+GA,+30602&entry=gmail&source=g>
> 315 Riverbend Road,
> <https://maps.google.com/?q=Georgia+%0D%0A+315+Riverbend+Road,+%0D%0A+Athens,+GA,+30602&entry=gmail&source=g>
> Athens, GA, 30602
> <https://maps.google.com/?q=Georgia+%0D%0A+315+Riverbend+Road,+%0D%0A+Athens,+GA,+30602&entry=gmail&source=g>
> Tel: (706) 254-7958
> E-mail: [log in to unmask]
> ------------------------------
> *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
>
>
> Hi Lachele,
>
>
>
> 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.
>
>
>
> Many thanks,
>
> Neha
>
>
>
> *From:* Users of GLYCAM & GLYCAM-Web [mailto:[log in to unmask]] *On
> Behalf Of *Lachele Foley
> *Sent:* Wednesday, 13 June 2018 12:32 AM
> *To:* [log in to unmask]
> *Subject:* Re: ADD PHOSPHATE DERIVATIVE
>
>
>
> 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:
>
> Hi,
>
> 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.
>
> Regards
> Mohit
>
>
>
>
>
> --
>
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>



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