**From:** JC Gumbart (*gumbart_at_ks.uiuc.edu*)

**Date:** Mon Feb 05 2007 - 10:15:40 CST

**Next message:**Himanshu Khandelia: "too large an area/lipid in POPE bilayers using membrane plugin"**Previous message:**Klon, Anthony: "Calculation of CHARMM Parameters from GAMESS Output."**In reply to:**Klon, Anthony: "Calculation of CHARMM Parameters from GAMESS Output."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

If your frequency is in wavenumbers, shouldn't there be a factor of c^2 in

your equation as well?

Anyway, the conversion is 1 kcal/mol A^2 = 69.52 pN/A. You have to throw

Avogadro's number (6.022*10^23 atoms/mole) in there to make it work.

_____

From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf

Of Klon, Anthony

Sent: Monday, February 05, 2007 9:27 AM

To: namd-l_at_ks.uiuc.edu

Subject: namd-l: Calculation of CHARMM Parameters from GAMESS Output.

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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