AMBER Archive (2006)

Subject: Re: AMBER: heme improper torsions

From: David A. Case (case_at_scripps.edu)
Date: Mon Jan 16 2006 - 10:46:47 CST

On Mon, Jan 16, 2006, nkyx_at_sohu.com wrote:

> When I used xleap to prepare a system
> containing HEME, it gave me the message enclosed.

> Building improper torsion parameters.
> old PREP-specified impropers:
> <CYF 439>: -M CA N H
> <CYF 439>: CA +M C O

....

This message is for information purposes only. For the last dozen years or
so, Amber has always used all appropriate impropers (i.e. all those for which
parameters exist in the parameter file), and it ignores any impropers that are
specified in the input prepin files. It does print the values it finds, but
then does nothing else with them; the printout is essentially for debugging
purposes.

...good luck...dac

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