Subject: RE: question about nitro groups in AMBER

From: "Ross Walker" <ross[at]rosswalker.co.uk>
Date: Mon, 8 Nov 2004 09:50:05 -0800

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

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross[at]rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |