Re: initial structures for md simulations

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Wed Feb 16 2011 - 09:02:13 CST

For many proteins, PDB files are available for the protein data bank
http://www.rcsb.org/pdb/home/home.do

Structures for hydrocarbons are fairly easy to build by hand or with a
user generated shell script.

Crystal structures for many compounds are available from the Cambridge
Crystallographic Database
http://www.ccdc.cam.ac.uk/

Packmol is useful for assembly a variety of molecules into a single
simulation cell
http://www.ime.unicamp.br/~martinez/packmol/

oguz gurbulak wrote:
>
> /Dear All/,
>
>
>
> I want to generate some initial crystalline structures of my target
> molecules for md simulations. /Are there any /free softwares to do this?
>
>
>
> And are there any complete sources that give the theoretical
> structures of organic molecules ( like hydrocarbons ) determined by
> the experiments and give the x-ray, neutron scattering, NMR, IR or
> Raman results of organic molecules apart from the articles ? Could you
> please share your thoughts about this issue ?
>
>
>
> Thank you very much for your attention.
>
>
>
> Kind regards.
>
>

-- 
======================================================================
Jeffrey J. Potoff                         jpotoff_at_chem1.eng.wayne.edu
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
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