AMBER Archive (2006)

Subject: Re: AMBER: LEaP Warning ... when do NH2-neutral fragment

From: FyD (
Date: Tue Jun 13 2006 - 14:20:52 CDT

Quoting jitrayut jitonnom <>:

> Therefore, my question is
> how to check this error or where is the file that I should be check at first
> ?
> This is the warning in LEaP :
> > check as
> Checking 'as'....
> Warning: Close contact of 1.792161 angstroms between .R<ALD 1>.A<C 10> and
> .R<ALA 2>.A<N 1>

Just a close contact warning. Do not worry for that.

> Checking parameters for unit 'as'.
> Checking for bond parameters.
> Could not find bond parameter for: O - N
> Checking for angle parameters.
> Could not find angle parameter: O - N - H
> Could not find angle parameter: O - N - CT
> Could not find angle parameter: C - O - N
> There are missing parameters.

You need to load a force field parameter file using such LEaP command
FRCMOD = loadamberparams YOUR-FILE

See the amberX/dat/leap/cmd/frcmod.xx files for examples

regards, F.

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