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On Mon, Jun 13, 2016 at 4:18 AM, Xiaocong Wang <[log in to unmask]> wrote:
> Hi Manuel,
> Please see the following documentation page on glycam.org. We have
> protocols of altering charges when sugars are sulfated.
> This should solve your problem.
> Xiaocong Wang
> Complex Carbohydrate Research Center
> The University of Georgia
> 315 Riverbend Road,
> Athens, GA, 30602
> Tel: (706) 254-7958
> E-mail: [log in to unmask]
> From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of
> mmaestre <[log in to unmask]>
> Sent: Monday, June 13, 2016 4:01:09 AM
> To: [log in to unmask]
> Subject: problems with SO3 derivation
> Dear Glycam users,
> I'm having a bit of trouble building sulfo sialil-lacnac. To be clear, the
> structure I'm trying to build is the following:
> Written in Glycam06 compatible form (sort of):
> My problem is that I am not getting integral charges. I would expect to get
> an overall charge of -2 from xleap, however, I'm getting -2.031.
> I've checked all the units, and these are the individual charges:
> ROH: -0.194
> UYB: -0.194
> 3LB: 0
> 0SA: -0.806
> SO3: -0.837
> Ok, so, if I add all of it, indeed, I get -2.031. What's really annoying,
> though, is that it looks like the problem is on the SO3 or the UYB. I mean,
> if I construct any 6-sulfo-monoglycan, I'm going to be using a glycan
> fragment with net charge 0, an roh fragment with net charge -0.194, and an
> SO3 fragment with charge -0.837. Together, that's always going to be -1.031,
> which means that the charge will never ever be integral.
> Does anyone have any ideas? What am I doing wrong here?
> Thank you very much,
Athens, GA USA