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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.<br>
<br>
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:<br>
<pre>checking for GTK - version >= 0.99.7... no</pre>
<pre>*** The gtk-config script installed by GTK could not be found</pre>
<pre>*** If GTK was installed in PREFIX, make sure PREFIX/bin is in</pre>
<pre>*** your path, or set the GTK_CONFIG environment variable to the</pre>
<pre>*** full path to gtk-config.</pre>
<pre>configure: error: Cannot find proper gtk version</pre>
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.<br>
<br>
How do you all recommend I proceed once the CVS download is complete?<br>
<br>
Thanks for whatever help you can offer!<br>
<br>
Tommi Hassinen wrote:
<blockquote cite="midPine.A41.4.58.0502251023370.10048@messi.uku.fi"
type="cite">
<pre wrap="">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:
</pre>
<blockquote type="cite">
<pre wrap="">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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</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Heinz Hemken
Foster City, CA
</pre>
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