Re: fragment calculation from xray coordinates

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Re: fragment calculation from xray coordinates

From: Marcel Swart <m.swart_at_email.domain.hidden>
Date: Mon, 19 Sep 2005 09:24:04 +0200
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Hello Linda,

the "no transformation" error should also give you more information on
the
fragment for which the problem exists, just browse through the output to
find it.

The fastest way to solve it, is however to make a separate fragment file
for each of the six fragments that form the dication system, using for
each
fragment the atomic coordinates as they are in the overall (dication)
system.

This way there will be no "No Transformation" error, and you
immediately get
the energy differences between the two different conformations of the
fragments.

On Sep 19, 2005, at 2:17 AM, ldoerrer wrote:

> Hello all,
>  
> I'm trying to do a fragment calculation in ADF 2005.01 and cannot get
> past a
>  
> "no transformation found" error, which I understand means that the
> program cannot map between my fragments and the molecule.
>  
>
> I did the following:
>
> - Took the coordinates of 3 fragments from a crystal structure that
> form a cation. I am interested in the interaction between two cations,
> so there are two copies of each of the three fragments in my
> "molecule"
>
> - Took one example of each fragment and ran a single point calc to get
> the *.t21 files
>
> - Edited the run file containing all original coordinates so that each
> atom is assigned to one of the 6 fragments (2 copies of each of three
> fragmetns). I've double-checked the assignments and tried it with a
> high symmetry tolerance (0.1) and in both internal coordinates and
> cartesian.
>
> Is it possible to ask which coordinate/atom that is the problem? If
> the first is the problem, won't that suggest that the whole fragment
> has a problem, but if I have made an error, then some of the
> coordinates ought to be okay before the problem one is encountered ...
>
> Any suggestions are welcome.
>
> thanks for your help, Linda
>  
>
> Linda H. Doerrer
> Assistant Professor of Chemistry
> 602 Altschul
> Barnard College
> 3009 Broadway
> New York, NY 10027
> office: 212-854-2074
> fax: 212-854-2310
> ldoerrer_at_barnard.edu
>  
––––––––––––––––––––––––––––––––––––––––––––
dr. Marcel Swart

Theoretische Chemie
Vrije Universiteit Amsterdam
Faculteit der Exacte Wetenschappen

De Boelelaan 1083
1081 HV Amsterdam
The Netherlands

Tel +31-(0)20-5987619
Fax +31-(0)20-5987629
E-mail m.swart_at_few.vu.nl
Web http://www.few.vu.nl/~swart
––––––––––––––––––––––––––––––––––––––––––––
Received on 2005-09-19 09:24:23

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