Subject: CCL: question about nitro groups in AMBER

From: khunter$at$mta.ca
Date: Fri, 5 Nov 2004 11:18:06 -0400

In AMBER each atom has a designated type which is defined to set of parameters 
in AMBER.  It appears that nitro groups are not able to be characterized by 
the existing atom type definitions.  Are NO2 groups able to be studied with 
AMBER?  Have the parameters for NO2 been determined previously?  Is it 
possible to define your own parameters manually and if so how?  Is there a 
systematic method to how parameters are defined in AMBER?  Any assistance 
would be greatly appreciated.

Ken Hunter
Mount Allsion University

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From: "David A. Case" <case$at$scripps.edu>
Date: Fri, 5 Nov 2004 09:15:48 -0800

On Fri, Nov 05, 2004, khunter$at$mta.ca wrote:

> In AMBER each atom has a designated type which is defined to set of
> parameters in AMBER.  It appears that nitro groups are not able to be
> characterized by the existing atom type definitions.  Are NO2 groups able to
> be studied with AMBER?  Have the parameters for NO2 been determined
> previously?  Is it possible to define your own parameters manually and if so
> how?  Is there a systematic method to how parameters are defined in AMBER?
> 

Amber does have a systematic way of handling pretty arbitrary organic
compounds, although I don't personally know how well it performs for nitro
groups.

Take a look at chapter 4 of the Users' Manual, available at
    http://amber.scripps.edu/doc8/amber8.pdf

...good luck...dave case