| PROGRAM | PURPOSE |
| avNgrids.f | The program to read N grids in UHBD format and write their average, useful in combining results from sdabf, or simply converting from ascii to binary and vice versa. type "avNgrids" to learn about usage of the program. |
| chk_rxna.f | computes distances between atoms listed in 2 rxn files |
| cmpgrds.f | compares 2 grids, writing information about differences |
| da-pairs.f | tabulates donor-acceptor pairs, creating reaction atom pairlist |
| gen_ran1.f | prints out 1000 random numbers used in BD program |
| grid2i.f | the program to convert grid files from UHBD/GRID to InsightII format |
| his2his.f | makes the sda history file sparser. Re-writes a history file (read from standard input) to the standard output so that the time step between the output trajectory coordinates approximately equals the number read from the command line (in ps). |
| his2pdbs.f | converts sda file with translational and rotational coordinates of complexes to a set of pdb files. Reads control data from standard input as from 3 lines for: pdb file of the second protein, history file (fort.55) from sda, the first letter for a set of pdb files to be produced. Writes also a file "4insight.log" - template of InsightII source file to generate a set of rgb files with the snapshots of the proteins motion during BD. |
| last2rates.f | calculates rates from incomplete sda output |
| mk_ds_grd.f | makes charge desolvation penalty grid. Input read from standard
input is:
spacing, 3 dimensions (x,y,z) of the grid; ionic strength, solvent dielectric, ion exclusion radius; the name of the pdb file, the name of the desolvation penalty grid file to write and its format (0/1 means binary/ascii). The input data is separated by comment lines. |
| os2rates.f | combines sda outputs to one rate + dispersion, icomm=2,3. The results are written in fort.61. sda output files need to be copied to the files fort.11, fort.12 and so forth. |
| os12rates.f | combines sda outputs to one rate + dispersion, icomm=1. The results are written in fort.61. sda output files need to be copied to the files fort.11, fort.12 and so forth. |
| extractdata.f | extracts data from 1 sda output to scaled 2 and 3 contact rates and residence times |