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

From: David A. Case <case.scripps.edu>
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?

....dac 

-- 
==================================================================
David A. Case                     |  e-mail:      case.scripps.edu
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            |    http://www.scripps.edu/case
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Apr 20 2004 - 21:53:00 PDT
Custom Search