[ghemical-devel] C-I parameters

[Heinz Hemken]

I believe this problem occurred with an aromatic C to I bond in 
levo-Thyroxine. The C-I bond that results is way too short, almost the 
same as a C-H bond.

BTW, I am having problems compiling 1.01 again, having forgotten how I 
resolved the problem a few months ago. I get the following error during 
./configure:

checking for GTK - version >= 0.99.7... no

*** The gtk-config script installed by GTK could not be found

*** If GTK was installed in PREFIX, make sure PREFIX/bin is in

*** your path, or set the GTK_CONFIG environment variable to the

*** full path to gtk-config.

configure: error: Cannot find proper gtk version

I have installed gtkglarea-1.2.2-19.i386.rpm and gtkglext-1.0.6 (I'm 
getting desperate), without success. The gtk-config script does not 
appear to exist on my ssytem (I searched for it with "find"). I am 
currently checking out the ghemical module from the bioinformatics.org 
CVS repository. I am using fedora core 3, so I don't have the old GTK.

How do you all recommend I proceed once the CVS download is complete?

Thanks for whatever help you can offer!

Tommi Hassinen wrote:

>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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>>
>>    
>>
>
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>  
>


-- 
Heinz Hemken
Foster City, CA

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