Dear Amber 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:
NeuAc-alpha-2-3-Gal-beta-1-4-(6S)-GlcNac-Beta-1-ROH
Written in Glycam06 compatible form (sort of):
ROH-UYB(SO3)-3LB-0SA
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,
Manuel
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Received on Mon Jun 13 2016 - 01:30:02 PDT
