AMBER Archive (2009)

Subject: [AMBER] a problem in building oligosaccharides using LEaP

From: Song Lin (songlin_at_moon.ibp.ac.cn)
Date: Thu Dec 24 2009 - 20:12:10 CST

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.
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Beijing, 100101
P.R.China

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