Calculate J-coupling values from specified dihedral angles.

jcoupling <mask> [outfile <filename>] [kfile <param file>] [out <filename>] [name <dsname>]

<mask> Atom mask in which to search for dihedrals within.
[outfile <filename>] File to write j-coupling values to with fixed format.
[kfile <param file>] File containing Karplus parameters (default is $AMBERHOME/dat/Karplus.txt).
[out <filename>] File to write data set output to.
[name <dsname>] Data set name.

Note data sets are not generated until run is called.

Calculate J-coupling values for all dihedrals found within <mask> (all atoms if no mask given). In order to use this function, Karplus parameters for all dihedrals which will be calculated must be loaded. By default cpptraj will use the data found in $AMBERHOME/dat/Karplus.txt; if this is not found cpptraj will look for the file specified by the $KARPLUS environment variable.

In the Karplus parameter file each parameter set consists of two lines for each dihedral with the format:


The first line defines the parameter set for a dihedral. <Type> is optional; if not given the form for calculating the J-coupling will be as described by Chou et al.; if ’C’ the form will be as described by Perez et al. The <NameX> parameters define the four atoms involved in the dihedral. Each <NameX> parameter is 5 characters wide, starting with a plus ’+’, minus ’-’ or space ’ ’ character indicating the atom belongs to the next, previous, or
current residue. The remaining 4 characters are the atom name. The parameters <A>, <B>, <C>, and <D> are floating point values 6 characters wide describing the Karplus parameters. For the ’C’ form A, B, and C correspond to C0, C1, and C2; D is unused and should not be specified. The second line is a list of residue names (4 characters each) to which the dihedral applies.

For example:

C HA CA CB HB 5.40 -1.37 3.61

Describes a dihedral between atoms HA-CA-CB-HB using the Perez et al. form with constants C0=5.40, C1=-1.37, C2=3.61 applied to ILE and VAL residues.

Output can be in both a fixed format (outfile <filename>) and using cpptraj data set/data file formatting (out <filename>). The fixed format has each dihedral that is defined from <mask1> printed along with its calculated J-coupling value for each frame, e.g.:

#Frame 1
1 SER HA CA CB HB2 45.334742 4.024759
1 SER HA CA CB HB3 -69.437134 1.829510

First the frame number is printed, then for each dihedral: Residue number, residue name, atom names 1-4 in the dihedral, the value of the dihedral, the J-coupling value. In cpptraj format, only the J-coupling value is written.