**From:** Klon, Anthony (*aklon_at_pcop.com*)

**Date:** Mon Feb 05 2007 - 09:27:09 CST

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I have a rather silly question. I've been trying to calculate CHARMM

parameters for a small molecule that isn't defined in any of the

topology / parameter files. Although CHARMM parameters can be built up

in an additive fashion, there are still some groups and hence some atom

bond lengths / angle terms which are not defined.

Geometry optimization of these fragments proceeded smoothly in GAMESS,

and once a stable point was obtained, the full Hessian matrix was

calculated and the frequencies were extracted.

Here's the problem:

To calculate the bond force constant from a frequency, it seems as

though it should be a straightforward exercise:

k = 4 * pi ^ 2 * u * v ^ 2

where u is the reduced mass, and v is the frequency (actually, GAMESS

outputs the wavenumber in cm ^ -1).

The first problem is that I can't seem to get my units to match up.

GAMESS reports frequencies in cm ^ -1, and reduced masses in amu (atomic

mass units). The constants in the CHARMM parameter files are in units of

kcal / mol / Ang. ^ 2.

The wavenumbers can obviously be converted into angstroms, and the amu's

into units of kcal, but this still leaves something out (namely that

there are no moles in the calculated result!).

I know that other NAMD users must have dealt with the same problem. I'm

probably missing something trivial, but don't know what it is.

Sincerely,

Anthony

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