The DOT charges (.amber) file

The utilities supplied with DOT (e.g. pdb_to_dot) use an input file containing the partial charge and the radius for every atom present in both the still and the moving molecule. For our testing example we drew charges/radii from the AMBER table (see http://www.amber.ucsf.edu/amber).

The DOT charges/radii file format doesn't correspond to the strict AMBER format, and changes were made to adjust it to the format readable by UHBD. The charges/radii file should consist of the header (2 first lines) and the charges/radii table. The header is not analyzed while processing with DOT utilities, but UHBD requires the following header:

AMBER
resi atom chrg epsi sigm radi end

Immediately after the header should follow a table of 6 fields separated by spaces. Here is the description of the table:

field #1 : residue name
field #2 : atom name
field #3 : the partial charge of an atom
field #4 : ignored, but must be present
field #5 : ignored, but must be present
field #6 : the radius of an atom

Here are few sample lines from a .amber file:

AMBER
resi  atom   chrg   epsi   sigm   radi end  
ALA   N    -0.520  0.100  3.029  1.515 
ALA   H     0.248  0.020  1.782  0.100 
ALA   CA    0.215  0.000  3.296  1.648 
ALA   CB    0.031  0.100  3.564  1.782 
ALA   C     0.526  0.100  3.296  1.648 
ALA   O    -0.500  0.200  2.851  1.425 
GLY   N    -0.520  0.100  3.029  1.515 
GLY   H     0.248  0.020  1.782  0.100 
GLY   CA    0.246  0.100  3.421  1.711 
GLY   C     0.526  0.100  3.296  1.648 
GLY   O    -0.500  0.200  2.851  1.425