Re: Kanamycin topology

From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Aug 17 2009 - 09:53:25 CDT

Dimitry,

If you want to generate a topology for use in CHARMM, I would suggest
perusing the CHARMM doc files.

If you want to generate a topology for use in NAMD, you could look at the
following tutorials:

http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html
http://www.ks.uiuc.edu/Training/Tutorials/vmd/vmd-tutorial-files/

http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-files/

http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/
http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-files/

http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/
http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-tutorial-files/

Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Wed, Aug 12, 2009 at 12:16 PM, DimitryASuplatov <genesup_at_gmail.com>wrote:
> Hello,
>
> I need a kanamycin topology to run in charmm. I could not find any in
> charmm files or in the internet.
> 1/ Are you aware of such topology to be already prepared by someone?
> 2/ Could you explain to me the basic steps of preparing a topology for
> charmm?
>
> Thank you for your time.
>
> SDA
>
>

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