Re: [AMBER] Query about the Glucose Parameters

From: David A Case <>
Date: Fri, 24 Nov 2017 17:11:03 -0500

On Fri, Nov 24, 2017, Aashish Bhatt wrote:
> In the 0GA+ROH library,OH-O is not binding in the preparation of topology
> and coordinate file. but is getting bound in equilibration.

This looks a lot like the case one can have when there is no Lennard-Jones
(vdW) term on a H atom, and it can move arbitrarily close to a nearby oxygen
atom. You should check the electrostatic energy at the point around where the
OH-O distance goes almost to zero: does it become very negative?

If you have not done so, try turning on SHAKE for hydrogens (ntc=2). If the
dagnosis in the above paragraph is correct, that should prevent this from

[I'd like to encourage all Amber users to switch to gaff2, where there are no
longer any hydrogens with zero vdW parameters.]

...hope this helps....dac

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Received on Fri Nov 24 2017 - 14:30:03 PST
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