RESP Demos: 

Four cases are provided which covers the range of posiblities.

  water		One molecule with a single stage fitting

 ethylene	One molecule with a two stage fit on a single conformation

 bis-napthyl 	One molecule with a two stage fit on two conformations

  adenine	Two molecules fitted together to get charges for a 
		"super molecule".

 peptoid	Two stage fit of a peptide-type residue to be consistent
		with Cornell et al. '95 peptides


Some remarks on these demos by Wendy Cornell:

1)  ethylene -- This only requires a one-stage fit since there
are no methyl or methylene groups.  Both the carbons and
the hydrogens should be constrained to be equivalent in stage 1.

2)  adenine -- This is a 2-conformation fit.  In stage 1, I would 
not make methylene H21 equiv between the 2 confs and methylene
H22 equiv between the 2 confs.  They get refit in stage 2
and are made to be equiv within each conformation at that time.
When 2 different conformations are used in the fit (I don't think 
that's the case here) then H21(mol 1) may not correspond
rigorously to H21(mol 2) anyway.  My general philosophy was the 
fewer constraints in stage 1, the better.  Although I usually 
made the C's in methyl and methylene groups be equiv in
stage 1 just to "nail down" part of the charge distribution.

In stage 2, H22 was constrained to be equal to H22 instead of H21.
I would really like to see the atomic numbering appear in the
input files.  I always end up writing it in anyway by hand,
otherwise I make mistakes like the above.

3)  bis-napthyl -- What is that extra lagrange constraint doing 
at the end of the first input file?

Again, I wouldn't make each H within the methyl and methylene
groups be equiv to its coresponding atom in the other
conformation in the first stage.

4)  The input files don't always have the proper title
(i.e. "water," "adenine", etc)

The weakest aspect of the RESP model, in my opinion,
is that the second stage fit was initially employed
to refit inequivalent atoms (methyl H's), but then
was also used to pull down the charges on the
nonpolar atoms even further through use of the stronger 
restraint.  The obvious problem is how to handle
polar atoms which are not equivalent but need to be.
This turned out not be a problem with amino H's, for example,
but there may be other systems where it is a problem.  At 
the very least, it means the philosophy and purpose of the 
second stage is not well defined.  Chris wanted to include methine
groups in the second stage refit, but it was found that the 
stronger restraint reduced the charges too much and adversely 
affected the fit.  If we had it to do over again, I'd say
just use the same restraint in both stages (and I think Chris
came to the same conclusion.)

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