AMBER Archive (2004)

Subject: Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations?

From: David A. Case (
Date: Tue Apr 20 2004 - 15:29:47 CDT

On Tue, Apr 20, 2004, Ilyas Yildirim wrote:
> After using gaussian, I checked out the result in MOLDEN. The molecule is
> on a 2-D surface, not in a 3-D.

Yes--the x-coordinate of every atom is 1.0; that will put things in a plane.

> I do not understand why this happens.

Nor do I, and I have not real way of knowing how/why that happened, since I do
not know how you created your Gaussian input file.

> The .pdb file I am using is either a cytosine or isocytosine taken from CCD
> database.

Are you sure this is in a correct PDB format?



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to