Subject: Cartesian vs DLC

From: Dmitry Kovalsky <[email-masked]>
Date: Mon, 2 Dec 2002 18:56:20 +0200

Dear CCL,

While performing structure optimization of the enzyme's active site (two 
identical chains each of 4 residues interconnected by 4 h-bonds) with bound 
Na+ ion to it,  I have noted that the choice of coordinates (CART or DLC) to 
be used dramatically infulences the final geometry. 

In case of DLC coordinates the distance between these two chains increses in 
few Angstroms while Na+ almost immobile. In contrast when the Cartesians is 
used the Na+ moves a lot and the active site moves very little.

Is it Ok? 
What result should I believe?  

Sincerely yours,

Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143
UKRAINE

E-mail: [email-masked]
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589

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From: Mikael Johansson <[email-masked]>
Date: Mon, 2 Dec 2002 20:32:37 +0200 (EET)

Hello Dimitry and All!

> What result should I believe?

Usually the one with the lower energy is the better geometry. But when
modelling an enzyme it might not be what you really want. You could try
to do a Cartesian based optimization on the structure optimized with
internal coordinates, and vice versa, and see what happens to the
structure.

As a side note, it's a good idea to specify what program you are using,
it usually makes answering easier :-)

Have a nice day,
    Mikael J.
    http://www.helsinki.fi/~mpjohans/

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From: "Reynier Suardiaz del Río" <[email-masked]>
Date: Sat, 2 Dec 2000 13:10:05 +0000

I'm trying to build the parameters for a MD simulation of an 
epoxidic sistem but a have not found any experimental data of the 
raotational barrier for the dihedral angle H1-C2-C3-C4 in the 
following sistem:

                        _

 I'll be gratefull of any suggestion.

 _____________________________________________

 Reynier Suardiaz del Rio
 Department of Physical Chemistry
 Chemistry Faculty
 University of Havana
 email: [email-masked], [email-masked]
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