AMBER Archive (2004)

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

From: Wen-Chi Tseng (
Date: Thu Aug 12 2004 - 04:16:38 CDT

On Tuesday 10 August 2004 10:53 pm, Karl N. Kirschner wrote:

> These charge errors are a result of rounding.
> 4GA should have a zero charge, OME should have a -0.194, and 1GA
> should have +0.194. To get a perfectly neutral system, alter the
> charge on 1GA C1 and the 4GA C4 appropriately.

I did a minor adjustment of the charges of these two atoms. And it
works. Now I can construct a neutral oligo. But I still cannot remove
the bad contacts after a 50 ps MD in implicit water.

BTW, could you advise why the charges of these two atoms need to be
changed? Do I need to do such charge adjustments for different types
of polysaccharides, such as heparin? If so, please advise a general
guideline. Thanks.



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