RE: question about nitro groups in AMBER

Dear Ken,
 > 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?
 Yes, as long as you provide the missing parameters.
 >Have the parameters for NO2 been determined
 > previously?
 I don't know if there are published parameters available, a literature
 search may turn up some useful results. However, it should be fairly easy to
 come up with your own parameters. Chapter 12 of the Amber 8 manual has a
 section on parameter development. At a first guess you can simply calculate
 equilibrium bond lengths and force constants from QM calculations. The same
 with angles and dihedrals. As for charges this is a completely automated
 method. See http://www.u-picardie.fr/labo/lbpd/RED/ for a program that
 will
 do it for you.
 You could also use the Generalised amber force field GAFF along with the
 antechamber program that is provided with Amber8. The GAFF force field is
 designed to study drug like molecules etc both in solution and in protein
 environments. In this way you can do mixed simulations, e.g. using the FF99
 amino acid force field for a protein and the GAFF force field for a
 coenzyme...
 >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.
 You should check out the Amber tutorials
 http://amber.scripps.edu/tutorial/index.html
 You could also take a look at this 'provisional' tutorial which explains
 how, once you have your parameters, you can use xleap to define non-standard
 residues and build prmtop and inpcrd files for non-standard systems.
 http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/index.htm
 All the best
 Ross
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 |\oss Walker
 | Department of Molecular Biology TPC15 |
 | The Scripps Research Institute |
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