The AMMP Language

The general syntax of the AMMP language is:

keyword parameter(s) ; for a command and

# anything ; for a comment.

label: ; for a loop label or jump target.

The ';' is a required termination character.

Parameters can be explicit numbers (1.00), predefined variables (x), or indexed atomic parameters (i.x is the x coordinate of the atom with serial number i and 1.q is the charge of the atom with serial number 1).

AMMP is not case sensitive. Commands can span several lines, but each keyword must be contiguous.

Atoms are assigned a unique integer serial number and referred to by this number. For polymers 100*residue number + atom_number_in_the_residue is used. This makes it easy to convert between serial number and atomic residue. With 32 bits you will run out of memory well before you will run out of integers. Atom names are given by convention as residue.atom (i.e. "ala.ca"). IF THESE CONVENTIONS ARE NOT FOLLOWED THEN AMMP WILL RUN, BUT WILL PRODUCE INCORRECT PDB FILES AND HAVE DIFFICULTY REFERENCING ATOMS BY NAME.

Commands by function List the commands roughly grouped by their functions.