Subject: bond stretching force constant from QM data

From: Valentin Gogonea <[email-masked]>
Date: Sun, 26 Jan 2003 08:49:42 -0500

Dear CCLers and GMX users,

I am trying to estimate the force constant for Fe-S bond stretching 
> from QM calculations and use it with Gromos87 force field (gromacs). I 
carried out UB3LYP/6-31+G** calculations for Fe-SCH3 
(charge=+1,multip=5) and Fe-Imidazole (+2,5) with G98 and I got the 
following force constants (I used a conversion factor from mDyne/A to 
KJ/(mol nm2) of 60230):
		mDyne/A		kJ/(mol nm2)		Gromos87
Fe-S		1.839		110763
Fe-N		0.757		45594			418400

1) Is it acceptable to scale properly (using the QM and Gromos Fe-N 
force constants) the Fe-S force constant  to be in the same range as 
the Fe-N force constant in the Gromos87 force field. Did anybody use 
this kind of approach or there is a better way to estimate and adjust 
the QM determined force constant to a force field force constant?

2) For an angle bending the force constant required in the forcefield 
has units of kJ/(mol rad2), while the one obtained from QM calculations 
has units of kJ/(mol nm2). I believe that the former can be obtained 
> from the latter if one assumes that the oscillator length for this 
particular normal mode is the distance between the endpoints of the 
angle. This should be valid for a torsion angle too. Is this correct?

I would appreciate any insight that I can get from the list and I thank 
you for your help.

Valentin Gogonea
Department of Chemistry
Cleveland State University

From: "David J Anick" <[email-masked]>
To: [email-masked]
Subject: How to resolve overlapping Gaussians in the UV Spectrum?

Date: Sun, 26 Jan 2003 17:53:24 -0800

Dear CCL-ers,

I have a complex line shape from a spectrum that I would like to
represent as a sum of overlapping Gaussians.  More precisely,
I have a function y=f(x), a < x < b, given as about 500 (x,y)
points, where f(a)=f(b)=0, and I would like to find a small
number (typically 3 to 8, perhaps) of Gaussians whose sum
approximates f.  I.e. I want to generate parameters {c_i,s_i,b_i}
for which the function
          F(x) = SIGMA_i  c_i exp(-s_i*(x-b_i)^2)
is a very good approximation to  f.

Can anyone please point me to software, free or not, Linux or
Windows, that can do this?

Thank you.  I will summarize responses.

David Anick PhD MD
[email-masked]
(Harvard Medical School)