The moving molecule (.dot) file

The first step in the preparation of the moving molecule file is to strip non-polar hydrogen atoms following the directions given for the still molecule. The moving molecule description consists of a single file describing the Cartesian coordinates of each atom and its partial charge. DOT uses this file for the moving molecule charge distribution, and also to generate the moving molecule mask. DOT automatically generates the moving molecule mask by replacing each partial charge with the value of "1". In this manner, each atomic center is occupied by the mask value of 1. Since the moving molecule mask is generated from the moving molecule charge distribution, only one moving molecule file is required by DOT (the *.dot file).

In order to create the moving molecule charge file, use the DOT utility pdb_to_dot:

pdb_to_dot pdb_filename charge_filename dot_file.dot log_filename

The pdb_filename is the output from striph, as described above. The charge_filename is the same charge file used by striph (charges.amber is supplied with DOT), and the .dot file is the DOT input file. The log file stores information about the charge assigned to each atom.