Re: CCL: Concord/Corina replacements for Linux X-Enigmail-Version:

 Hi Andrew:
 If you don't wish to use CORINA at all (not even the 1 month free trial
 version), then you might like to try this.
 Lets say  you have *.cdx (chemdraw) files for 2D representation of your
 molecules. Take one of these at a time and open it in Chem3d. In chem3d, use
 edit --> select all to select all the atoms. Then, Tools ---> Cleanup
 Structure and then MM2 --> minimize energy. If your molecules are small
 enough, this process shall be fast. However, it takes a lot of time with MM2 if
 the molecules are big. Once you have minimized structure, then save as MDL
 molfile (*.mol).  The molfile will save the coordinates in 3D.
 I hope this helps.
 Sandeep Kumar
 Dr. Sandeep Kumar,
 Associate Research Scientist,
 Johns Hopkins University Department of Biology,
 106 Mudd Hall, 3400 N. Charles Street,
 Baltimore, MD 21218,  USA.
 Phone: 410-516-8433,
 Email: kumarsan$at$
 ----- Original Message -----
 From: "Andrew D. Fant" <fant$at$>
 Date: Wednesday, July 6, 2005 2:28 pm
 Subject: CCL: Concord/Corina replacements for Linux X-Enigmail-Version:
 > Good afternoon all, and thanks to everyone who responded to my
 > previousquestions about openbabel and descriptor code.  I have one
 > otherquestion about software that has come up.  Can anyone
 > recommend a
 > program that can generate 3D structures of any quality of all from 2D
 > representations?  I know that Concord and Corina can do this, but I am
 > doing this for my own education/edification and would rather not blow
 > the rent money on this project.  I'm hoping to take some data I have
 > pulled from various publications on my laptop on a train trip and
 > putterwith it en route, so a web-based tool is less than ideal.  If
 > anyone has
 > any suggestions, I would be most appreciative.
 > Thanks,
 > 	Andy
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