Re: Inorganic compounds

From: Chris Harrison (charris5_at_nd.edu)
Date: Wed Jan 14 2009 - 23:25:19 CST

This is an organic compound. Is the image missing some atoms .... the
counter-ion?

If the parameters are available, then NAMD can simulate the molecule.
Please look in the CHARMM forcefield to see if this is a possibility.

Alternatively, you can parameterize the molecule yourself. The paratool
plugin in VMD can be of help with this; however you will still need to
understand how to do the process manually. Please look at:

1. MacKerell, et al; J Phys Chem B 102:3586 (1998)
2. MacKerell, Wiorkiewicz-Kuczera, & Karplus; JACS 117:11946 (1995)

C.

-- 
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 Thu, Jan 8, 2009 at 12:20 PM, Casey,Richard
<Richard.Casey_at_colostate.edu>wrote:
>  Hello,
>
>
>
> We would like to run molecular dynamics simulations for the inorganic
> compound shown below (and attached) using NAMD/VMD.  Can inorganic compounds
> be modeled with NAMD?  If so, what would be an appropriate force field
> (Charmm? Amber? Other?)
>
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> --------------------------------------------
>
> Richard
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image002.jpg

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