Re: CCL:question about nitro groups in AMBER

["David A. Case" <case$at$scripps.edu>]

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