The PSF, CONS, and PARM keywords give the unit numbers of the comparison protein structure file, harmonic constraints, and parameter set; respectively. They must all be binary files created by a WRITE command to the main part of CONGEN, see Write Command. If any are not specified, the corresponding comparison data structure is presumed to be the same as the main data structure.
The COOR keyword specifies where the comparison coordinates come from and, optionally, where they are to be placed when the command finishes execution. The comparison coordinates can come from three sources; the main set, the comparison set in the main part of CONGEN, or from an external file. If the COOR option is left out or if you use the option MAIN, the comparison coordinates come from the main set. If you specify COMPARE in the COOR option, the coordinates come from the comparison coordinates in the main part of CONGEN, see Data Structures, and Coordinate Manipulations, for more details about this set. Otherwise, the coordinates will be read from a file. You are free to use either card image or binary files for these coordinates; but be sure that all coordinates you need are specified. See Read Coordinates, on the format of the coordinate files.
The NBOND and HBOND sub-commands are used to specify the comparison non-bonded and hydrogen bond list, respectively. The UNIT option is each of commands allows the specification of a Fortran unit number which refers to the binary file containing the lists. The COPY option requests that the main data structure be assigned to the comparison data structure. If neither option is specified, the program will generate a new list. The `nbond-specs', see Non-bonded Syntax, and `hbond-specs', see HBOND Syntax, specify generation and sigmoid switching function parameters.
When either of these data structures are read in, it is possible to modify the settings for the various switching function and energy evaluation parameters. Simply specify the values you want changed. You cannot change the selection method when something is read in (that doesn't make sense anyway). In the case of the hydrogen bonds, the file does not contain any of the selection and switching function parameters. If you specify a selection option, it will ignored even though you will get a message telling you what the values the program read are. Please ignore such information.
If any of the options or cutoffs for the HBOND or NBOND commands are not specified, the reference structure parameters will be used. If no HBOND or NBOND command is given, the list will be generated for a comparison PSF or coordinate set using the method employed for the reference structure.
The PBE keyword is used to specify the Poisson-Boltzmann data structure for the comparison structure. The data structure may be read from a disk file or may be recalled from an internal symbol. The UNIT keyword specifies that the Poisson-Boltzmann data structure be read from a binary file created using the PBE WRITE command, see PBE WRITE Command. The NAME keyword specifies that the data structure be taken from a symbol as specified by the PBE SAVE command, see PBE SAVE Command. If no option is specified and if the comparison PSF is the same as the main PSF, then the comparison PBE data structure will be assigned to the main PBE data structure