Re: AMBER: Energy minimization problem of -SO3H group

From: David A. Case <>
Date: Tue, 6 Nov 2007 21:12:08 -0800

On Tue, Nov 06, 2007, Takao Kobayashi wrote:
> I tried to optimize the structure of CH3-SO3H, but it failed,
> where H of S-O-H is overlapped on O of S=O.

This happens with phosphates as well. As far as I know, you will have to
correct this by hand, either by given non-zero vdW parameters to the
hydrogen, or by including an artificial S--H bond (say) to keep the proton
away from nearby oxygens. You might want to look to see how the ATP/GTP
parameters in the contributed parameters database handle this problem.

..good luck...dac

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Received on Wed Nov 07 2007 - 06:07:53 PST
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