4. AMMP commands


AMMP interpret commands with this syntax:




The command name is case insensitive and the number of arguments is typical for each command. The arguments must be separated with one or more spaces and the command must terminated by a semicolon (;) character. As shown in the following table, an argument can be:

Type Description
BOOL Boolean value (1 = true, 0 = false).

Character string. If it contains one or more spaces, you must use the single ' or double " quotes at the beginning and at the end of the string (e.g. "Hello World", or 'Hello World').


Floating point number with standard C syntax (the decimal separator must be a dot . and not a comma ,).


Unsigned float number.


Integer number.

LABEL Label for the program flow control (e.g. conditional jumps and loops). The labels must have a colon (:) at the end.

Unsigned integer number.


It could be a variable string name (integer or floating point), a constant (integer or floating point), an atomdata expression that could be:




where Serial is the atom serial number and Data is the atom data as reported in the following tables:

Data Description
x Cartesian coordinates.
fx Force components.
q Atom charge.
m Mass.
chi Elecronegativity.
Data Description
dx Minimization direction.
vx Velocity components.
a Non-bond terms.
jaa Self coulomb term.


In order to interpret much easier the syntax of the commands present in this guide, for each argument is highlighted its type (CHAR, FLOAT, INT, etc).



4.1 Command index

Command     Type     Description
ABC   Input   Define the angle - bond correlation.
ABUILD   Calc   Analytic geometry solver.
ACTIVE   Calc   Activate the atoms.
ADD   Math   Arithmetic sum between two terms.
ANALYZE   Calc   Evaluate the non-bond interaction energy.
ANGLE   Input   Define an angle.
ATOM   Input   Add a new atom.
AV5   Input   Define a tetrahedral "volume" or centroid.
BELL   Calc   Iterative distance geometry optimizer using the Bellman - Ford - Fulkerson algorithm.
BFGS   Calc   BFGS quasi-Newton minimizer.
BINDUMP   Output   Dump the specified term in binary or in base64 mode.
BOND   Input   Define a bond.
CLONE   Calc   Copy the current coordinate set and the active atom flag to the memory.
CLOSE   Output   Close the file opened with OUTPUT.
CNGDEL   Calc   Poliak-Ribeire conjugate gradient minimizer.
CONFIRMEND   Output   Confirm the end of the command execution.
COS   Math   Cosine trigonometric function.
DGEOM   Calc   Standard distance geometry optimizer.
DIPOLE   Calc   Calculate the dipole moment.
DIV   Math   Arithmetic division.
DOUBLETIME   Calc   Double the time scale in molecular dynamics.
DSCF   Calc   Direct SCF orbital optimizer.
DUMP   Output   Dump the specified terms to the current file.
ECHO   Output   Turn on/off the message/command echo.
EXIT   Flow   Quit AMMP.
EXPAND   Input   Expand an orbital.
FIX   Math   Round down to an integer.
FLUSH   Output   Flush the output.
GDOCK   Calc   Genetic algorithm rigid docking.
GENETIC   Calc   Genetic algorithm minimizer.
GRASP   Calc   Torsion space optimizer.
GSDG   Calc   Gauss-Siedel distance geometry optimizer.
HPAC   Calc   Total energy constrained molecular dynamics.
HYBRID   Input   Define a hybrid (improper) angle.
INACTIVE   Calc   Inactivate the atoms.
INDEX   Math   Get the serial number of the specified atom number.
INIT4D   Input   Initialize the fourd 4D potential (w coordinate).
JE   Flow   Jump if equal.
JES   Flow   Check the atom name and if it's equal to the string, jump to the label.
JG   Flow   Jump if greater.
JL   Flow   Jump if less.
JNE   Flow   Jump if not equal.
JNES   Flow   Check the atom name and if it's not equal to the string, jump to the label.
KOHONEN   Calc   Kohonen neural network geometry search.
LINMIN   Math   Search the atom direction for a minimum.
LOOPF   Flow   Define a floating point loop.
LOOPI   Flow   Define an integer loop.
MAX   Math   Find the maximum of two values.
MIN   Math   Find the minimum of two values.
MOM   Calc   Perform the MoM atomic charge calculation.
MOMADD   Calc   Select the atoms for MoM charge calculation.
MOMPAR   Input   Define the electronegativity and the self coulomb terms.
MONITOR   Calc   Perform a single point energy evaluation.
MORSE   Input   Define a morse bond.
MOV   Math   Set a variable to another one.
MUL   Math   Multiplication.
NOEGEN   Input   Set the noels to the current geometry.
NOEL   Input   Define the noe distance restraint.
NOP   Math   Dump the value of a variable.
NORMAL   Calc   Calculate the normal modes.
NZINACTIVE   Calc   Inactivate the atoms which aren't located at the axis origin (0, 0, 0).
ORBIT   Input   Define an orbital for SCF calculation.
OUTPUT   Output   Open a file for writing redirecting the output to it.
PAC   Calc   Predict and correct the molecular dynamics.
PACPAC   Calc   Iterated predict and correct the molecular dynamics.
POLYTOPE   Calc   Polytope simplex minimizer.
PPAC   Calc   Constant pressure molecular dynamics.
PRINT   Output   Print a message/variable to the current output stream.
PTPAC   Calc   Constant temperature and pressure molecular dynamics.
RANDF   Math   Pseudo-random number.
READ   Input   Read an AMMP command file.
RESET   Input   Reset all.
RESTORE   Calc   Copy a coordinate set and the active atom flag from the memory.
RESTRAIN   Input   Define a restraint between two atoms.
RICHARD   Calc   Thermodynamic path integrals using the Feynmann Weiner Kac approach.
RIGID   Calc   Polytope rigid body solver.
SERIAL   Math   Set a variable equal to the serial atom number given by the atom name.
SETF   Math   Define a floating point number variable.
SETI   Math   Define an integer number variable.
SIN   Math   Sine trigonometric function.
SQRT   Math   Square root.
STEEP   Calc   Steepest descent minimizer.
STEP   Input   Define a step distance (3 point noel).
SUB   Math   Subtraction.
SWARM   Input   Add a distance restrain to the mean distance.
TABLE   Calc   Create an empty sorted table for the table driven potential.
TABLEENT   Calc   Add a new element to the table.
TAILOR   Calc   Set, exclude, include the atoms from the non-bonded list.
TAN   Math   Tangent trigonometric function.
TBOND   Input   Define a bond which potential will be evaluated using the table method.
TETHER   Input   Tether an atom.
TGROUP   Calc   Define a torsion for the conformational search.
TIME   Math   Time for calculation speed measurement.
TJUMP   Calc   Boltzmann jump conformational search.
TMAP   Calc   Map two torsions rotating them systematically.
TMIN   Calc   Search the torsion angle.
TPAC   Calc   Predict and correct the molecular dynamics (constant temperature).
TRANDOM   Calc   Random conformational search.
TSEARCH   Calc   Systematic conformational search (grid scan).
TSET   Calc   Set the given torsion angle.
TRUNC   Calc   Truncated Newton method minimizer.
TRUST   Calc   Trust-region based minimizer.
TORSION   Input   Define a torsion angle.
TTARGET   Input   Define a torsion angle restrain.
USE   Calc   Select the force field terms for energy calculation.
V_MAXWELL   Calc  

Set the velocity distribution with a random Maxwell - Boltzmann distribution.

V_RESCALE   Calc   Rescale the velocities to a new temperature.
VELOCITY   Input   Set the velocity to the specified atom.
VERLET   Calc   Perform the leapfrogging molecular dynamics.
Calc = Calculation commands.
Flow    = Flow control commands.
Input = Input commands.
Output = Output commands.