Hi,
There is a problem when I build oligosaccharides using LEaP.
I just simply link the residues together:
glycan1=sequence{ROH 3VA 0SA}
glycan2=sequence{ROH 6VA 0SA}
When it's 2-3 bond(glycan1), it's OK; but when it's 2-6 bond(glycan2), I
got a disordered structure.
Maybe it's because when it's 2-6 bond, it contains a sequence like this:
-C5-C6-O6-C2-O6-C6-C5-
It contains two "-C2-O6-C6-C5-" in opposite direction.
And when LEaP automatically set the psi angle,
impose glycan2 {3 2} { {C2 O6 C6 C5 60.0} }
he doesn't know which subsequence to choose, so I got a bad structure.
Anyone knows how to deal with this problem? Any suggestion is welcome.
Thank you very much!
--
Center for Computational and Systems Biology,
Institute of Biophysics, CAS.
15 Datun Road, Chaoyang District
Beijing, 100101
P.R.China
Tel/FAX: 86-10-64888427
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Received on Thu Dec 24 2009 - 18:30:02 PST
