4. AMMP commands
AMMP interpret commands with this syntax:
COMMAND_NAME PARAMETER_1 PARAMETER_2 ... ;
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). | |||||||||||||||||||||||||||||||||
CHAR |
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'). |
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FLOAT |
Floating point number with standard C syntax (the decimal separator must be a dot . and not a comma ,). |
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UFLOAT |
Unsigned float number. |
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INT |
Integer number. |
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LABEL | Label for the program flow control (e.g. conditional jumps and loops). The labels must have a colon (:) at the end. | |||||||||||||||||||||||||||||||||
UINT |
Unsigned integer number. |
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VAR |
It could be a variable string name (integer or floating point), a constant (integer or floating point), an atomdata expression that could be:
Serial.data
where Serial is the atom serial number and Data is the atom data as reported in the following tables:
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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).
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. | ||
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. |
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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. | |