AMBER: Optimizing a structure and the interpretation of it

From: Ilyas Yildirim <>
Date: Sat, 24 Apr 2004 19:08:14 -0400 (EDT)

Dear Amber list members,

Usually people tend to optimize a structure using one of the ab initio
softwares like gaussian, jaguar or gamess before doing any kind of
calculations. My question is about how to see/think a structure. In the
PDB Databank or in the Cambridge Crystallographic Database, someone can
get a crystal structure. I was thinking that if somebody knows the crystal
structure of a molecule, there is no need to optimize the initial
structure. Namely, if you measured the structure experimentally, why to
optimize it? Using one of the molecules in CCD database I have calculated
the RESP charges for both cases: 1. without doing any kind of
optimization, 2. optimizing the structure and then calculating the
charges. There are differences at the results. Particularly, I have
done the calculations on a Cytosine molecule.

Comparing the charges on the base atoms, there is a charge difference of
..2 when the results are compared. The atoms at the sugar part changed .05.

My question is as following: When they do X-Ray diffraction to get a
crystal structure experimentally, is the final structure something like an
approximate structure? Or are we %100 sure that the atoms are oriented
the way it is described in these crystal structures?

At first, someone tends to think that the crystal structures are giving
the true positions of the atoms in the molecule. As a result, why to
optimize the structure.

But, it seems to me that the crystal structures are just approx.
structures, and in order to bring the structure to its natural real
conformation, someone needs to do quantum mechanical optimization.
Namely, someone needs to use an ab inition software to optimize the

I will appreciate if someone can give me some references which are related
to my question.


  Ilyas Yildirim
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Received on Sun Apr 25 2004 - 00:53:00 PDT
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