In the format for text parameter file, the data is divided into sections beginning with a keyword line and followed by data lines. The sections may be arranged in any order, and may divided up as well. Just prefix each set of data with the appropriate keywords. The format for each data section follow along with the necessary keywords. Please look at the parameter input files in the CGDATA directory for examples.
Keyword Format BOND - atom atom force_constant distance (2(A4,1X),2F10.0) THETA - atom atom atom force_constant theta_min (3(A4,1X),2F10.0) PHI - atom atom atom atom force_constant periodicity phi_max (4(A4,1X),3F10.0) IMPHI - atom atom atom atom force_constant i_phi_min (4(A4,1X),2F10.0) NBOND - atom polarizability n_effective_electrons vdW_radius (A4,1X,3F10.0) HBOND - atom atom well_depth distance (2(A4,1X),2F10.0)
Note that the data lines are NOT free field. However, you can add comments using the exclamation point, see Run Control. Sections end with the occurrence of another keyword or a line with the word END in columns 1-3, the latter terminating parameter reading. Blank lines are allowed in all the sections.
Some errors in the input file will result in warning messages but not termination of the run.
CONGEN will check for duplicate parameters. If all the corresponding values for a duplicate parameter are the same, then only a warning message is issued. Otherwise, an error message will be issued.
Any errors detected in the reading of the formatted parameter file will result in termination of the run, unless NOFAIL is specified on the READ command.
phi_max is either 0.0 or 180.0 for dihedrals with the minimum staggered
or eclipsed respectively.
If successive torsion angle or improper torsion angle parameters are specified with all four atoms and have the same atoms, this is a flag that the energy is to be computed as a sum of these multiple terms. For this special processing to be done, the PSF (or topology file used to generate the PSF) must have successively equal torsion or improper torsion angles which correspond to the parameters. In order to use this option, you must specify NOFAIL on the command line.
NBOND parameters must be present for all of the atom types. The program attempts to check this when reading either card image or binary parameter files.