[ghemical-devel] C-I parameters

[Tommi Hassinen]

Hello,

in ghemical-1.01 and on the current development version there indeed is
problems with iodine ; the bond length is defined only for aromatic iodine
compounds and for others a default (incorrect) bond length is selected.

To fix the problem, you have to find a file that contains the mol.mech.
bond length parameters, and do an addition there. In source packages the
file is

	bin/parameters/mm1param/stable/parameters1.txt

You may also modify a file that is installed in your system, in that case
it is probably one of these (change the version number to match the one
you have):

/usr/share/ghemical/1.01/parameters/mm1param/stable/parameters1.txt
/usr/local/share/ghemical/1.01/parameters/mm1param/stable/parameters1.txt

Then find this line from the file:

0x0603 0x3500 S 2.050  490.0

Then duplicate it three times, and modify the first number like in here:

0x0600 0x3500 S 2.050  490.0	//added 20050225
0x0601 0x3500 S 2.050  490.0	//added 20050225
0x0602 0x3500 S 2.050  490.0	//added 20050225
^^^^^^
these numbers are changed ; the comment added above is not necessary.

Then just save the file, and the parameters are added. The number 0x3500
corresponds to iodine, and the 0x06?? numbers correspond to different
carbon types. The paramters for aromatic carbon are just copied for all
carbon types.

If you made the change in a source package, then recompile and install as
usual (you have to do the "make install" as well).

I hope this helps,

	Tommi


On Thu, 24 Feb 2005, sandra antunez wrote:

> Hi,
>
> When I minimize an iodine-containing molecule I get a Caromatic-I lenght
> of around 1.1A. I wonder if there is a way to get better distances.
>
> Thanks,
>
> Sandra
>
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