----- Forwarded message from "B. Lachele Foley" -----
Date: Mon, 4 Jan 2010 16:30:07 -0500
Subject: Re: [songlin.moon.ibp.ac.cn: [AMBER] a problem in building
oligosaccharides using LEaP]
From: "B. Lachele Foley"
I just tried building the ROH 6VA 0SA sequence. I used the builder
and amber10's tleap and the 20091214 version of sleap. All built the
sequence just fine (well...except for the slightly wonky angles that
sleap creates). I even tried using the impose command to see if there
is a problem, but it works fine. I don't get a disordered structure.
I'm not sure what to suggest is wrong.
> ----- Forwarded message from Song Lin <songlin.moon.ibp.ac.cn> -----
>
> 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!
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Received on Tue Jan 05 2010 - 05:00:02 PST
