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

From: David A. Case <>
Date: Tue, 20 Apr 2004 13:29:47 -0700

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
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Received on Tue Apr 20 2004 - 21:53:00 PDT
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