Re: AMBER: Optimizing a structure and the interpretation of it

From: Kazuo Koyano <>
Date: Mon, 26 Apr 2004 14:14:25 +0900

Dear Ilyas Yildirim;

 As a crystallographer, I should like answer to your question briefly as
possible as I could.
First, a molecular crystal to which most organic molecules belong, is formed
by a weak force as Van der Waals.
Imagine the crystallization process. Now a days, an isolated small molecule
taken from a crystal on CCD database has a precise structure as it is. So as
you say, it is generally not necessary to optimize the structure, but in
vacuum or rotated about a bond for examples, optimization would be
 Second, X-ray are scattered by electrons of atoms. For a large molecule
like protein, it is very hard to detect hydrogen that has only one electron
even if strong X-ray as radiation light is used. Then, adding hydrogens to a
protein from PDB Databank, the got structure has to be optimized.
 I hope and believe strongly that molecular dynamics would simulate not only
a simple cubic cell but also a general crystal lattice cell as a periodic
boundary condition, that is crystal structure itself in the near future.
good luck

Kazuo Koyano

Center for Collaborative Research, The University of Tokyo
4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, JAPAN

----- Original Message -----
From: "Ilyas Yildirim" <>
To: <>
Sent: Sunday, April 25, 2004 8:08 AM
Subject: AMBER: Optimizing a structure and the interpretation of it

> 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
> structure.
> I will appreciate if someone can give me some references which are related
> to my question.
> Best,
> --
> Ilyas Yildirim
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Received on Mon Apr 26 2004 - 08:53:00 PDT
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