Subject: Amber force field parameters

From: [email-masked] (Dick Swenson)
Date: Sat, 09 Sep 1995 10:50:32 -0400

I have been attempting some molecular mechanical calculations using the 
AMBER force field utilizing the Hyperchem software on the small molecule 
flavin mononucleotide within certain flavoproteins.  Attempts to perform 
these calculations while including the FMN cofactor generates a series of 
error messages due to the lack of parameters within the amber89 force field 
parameter sets, my most recent set.  Does anyone have values for the 
following bonds, bends, angles or can you tell me how to estimate them?  
Also, I am somewhat confused about the correct atom type assignment for the 
carbon atoms for the central pyrazine ring of the isoalloxazine ring.  
Should they be CA, CB or CM?  (The following parameters would be needed for 
the CM atom type for the carbon atoms bridging the pyrazine and pyrimidine 
rings and the CA atom type for the carbon atoms bridging the o-xylene and 
pyrazine rings as Hyperchem assigns them.) Thanks for the help.

Stretch parameter for:
type NC-CM
type CA-N*

Bend parameter for:
types NC-CM-CM
types NC-CM-N*
types NC-CM-C
types NC-CA-CA
types CA-NC-CM
types CA-CA-N*
types CA-N*-CM
types CA-N*-CT

Torsion parameter for:
types C-NC-CM-CM
types C-NC-CM-N*
types C-CM-NC-CA
types CA-CA-N*-CM
types CA-CA-N*-CT
types CM-CM-NC-CA