Re: CCL: Concord/Corina replacements for Linux X-Enigmail-Version:
0.90.2.0
- From: SANDEEP KUMAR <skumar23$at$jhem.jhu.edu>
- Subject: Re: CCL: Concord/Corina replacements for Linux
X-Enigmail-Version: 0.90.2.0
- Date: Wed, 06 Jul 2005 15:43:11 -0400
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.
Sincerely,
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$at$jhu.edu.
URL: http://myprofile.cos.com/Kumarsan.
or https://jshare.johnshopkins.edu/skumar23/public_html/
----- Original Message -----
From: "Andrew D. Fant" <fant$at$pobox.com>
Date: Wednesday, July 6, 2005 2:28 pm
Subject: CCL: Concord/Corina replacements for Linux X-Enigmail-Version: 0.90.2.0
> 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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