AMBER Archive (2008)

Subject: Re: AMBER: sp carbon notation?

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 18 2008 - 19:22:14 CDT

On Wed, Jun 18, 2008, Laura Benton wrote:
>
> How do I signify an sp hybridized carbon in the molecule specification
> section? I looked in the referenced AMBER paper (from Cornell et. al)
> and did not find that information anywhere.

Standard proteins and nucleic acids don't have any sp carbons, so you won't
find them in Cornell et al.

The GAFF force field is designed for "arbitrary" organic molecules, and it
has a type, "c1", for sp-hybridized carbons.

...hope this helps....dac

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