AMBER Archive (2004)

Subject: Re: AMBER: how to correct the charge of oligosaccharides

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 10 2004 - 09:31:40 CDT

On Tue, Aug 10, 2004, Wen-Chi Tseng wrote:
>
> I also saved these oligos in pdb file, and used vmd, swiss-pdbViewer,
> and xleap to visualize the molecules. These structures could be seen
> correctly only under xleap. Under vmd and spdbv, incorrect linkages
> were found. Does anyone know how to fix this?
>

LEaP uses the connectivity information in the libraries to draw bonds, but
vmd and Swiss-PDB infer bonds from interatomic distances. Hence, if you have
bad contacts in your structure, the latter two programs draw these as bonds.
So once you fix the coordinate problem, the viewing problem will probably get
fixed as well.

...good luck...dac

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