Intermediate Files

These are files generated for the Molecule 0. In the file names, prefix0 is replaced by the actual prefix given in the input file to bd_top.

For Molecule 0, there are one or more OpenDX electric potential files from APBS. For each, there is generated a file ins-potential.xml , where potential.dx is the file from APBS. This is a grid file of integers (but in XML format) which denotes the interior (value of 1) and exterior points (value of 0) of the molecule. Likewise, for each file from APBS is generated a file born-potential.dx ; this is a grid of Born integral values used for the desolvation forces.

An analogous set of the above files is generated for Molecule 1.

The following files are generated for both molecules: