AMMP can be started typing ammp in the command prompt or using the full-featured graphic user interface implemented in VEGA ZZ. No command options are available starting it from the shell:
AMMP 2.1.0 - (c) 1993-2022, Robert W. Harrison VEGA edition by Alessandro Pedretti
AMMP is now waiting for the commands. Please remember that it accepts the standard input and output redirection and so you are able to control the software using a command file and to capture the output in another file:
ammp < COMMAND_FILE.amp > OUTPUT_FILE.out
Another possibility is the use of the command file as first argument:
3.1 The AMMP language
AMMP understands its own language having an easy syntax:
command PARAMETER_1 PARAMETER_2 PARAMETER_3 ... ;
The first word is the command keyword followed by required parameters which number depends on the own command. The expression must always terminate with the semicolon character (;).
cngdel 2000 0 0.01;
The parameters can be explicit numbers (e.g. 1.00),
predefined variables (e.g. x), or indexed atomic parameters (e.g. 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).
The comments can be introduced in the command files using the # character and they must be terminated by the semicolon:
# My comment;
The labels for loops and jumps can be specified using the colon (:) and the semicolon:
The 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. The atom names are given by convention as residue.atom (e.g. ala.ca).
If these conventions are not followed then AMMP will run, but it will produce incorrect PDB files and have difficulty referencing atoms by name.
The AMMP language is case-insensitive.