4.2 Calculation commands
There are the commands to perform AMMP calculations.
ABUILD (UINT)Niter
(UINT)FirstAtom (UINT)LastAtom
Analytic geometry solver. It use resultants to build atoms based on three or
more distances and the distance/planarity to build based on one or two
distances. The maximum number of atoms is 800.
Parameters:  
Niter  Number of iterations. If it's less then 1, one iteration only is performed.  
FirstAtom  First atom serial for selection.  
LastAtom  Last atom serial for selection. 
Return message:
Build steps.
Example:
ABUILD 50 1 95;
See also:
BELL, DGEOM, GSDG,
KOHONEN.
ACTIVE
(UINT)FirstAtom (UINT)LastAtom
Activate the atoms for the next calculations. The inactive atoms aren't considered and they are kept fixed.
Parameters:  
FirstAtom  First atom serial for selection.  
LastAtom  Last atom serial for selection. This is an optional argument. If it's omitted, LastAtom is the last atom in the molecule. 
Return message:
None.
Example:
ACTIVE 1 1200;
See also:
INACTIVE, NZINACTIVE.
ANALYZE
(UINT)FirstAtom (UINT)LastAtom
Evaluate the nonbond interaction energy, showing the complete nonbonded and electrostatic energies for the specified atom range ( IJ ). This command is useful for determining the interaction energy of a protein/substrate complex.
Parameters:  
FirstAtom  First atom serial for selection.  
LastAtom  Last atom serial for selection. This is an optional argument. If it's omitted, FirstAtom only is considered. 
Return message:
AMMP shows the energy for each atom in the selection range:
Vnonbon internal lys.n 137 Eq 12.860423 E6 1.397398 E12 2.191076 Vnonbon external lys.n 137 Eq 16.632879 E6 5.806829 E12 9.177713 Vnonbon total lys.n 137 Eq 3.772456 E6 7.204227 E12 11.368790
where internal is intramolecular energy, external is the intermolecular (interaction) energy, total is the sum of intramolecular and intermolecular energies, Eq is the electrostatic (coulombic) energy, E6 and E12 are the Lennard  Johnes terms. At the end of the atom dump, AMMP reports:
Vnonbon total internal 151.439880 Vnonbon total external 2.272158 Vnonbon total 153.712067 153.712067 nonbonded energy 153.712067 total potential energy
where Vnonbon total internal is the total intramolecular energy, Vnonbon total external is the total intermolecular (interaction) energy, Vnonbon total is the total nonbond interaction energy (it's the sum of Vnonbon total internal and Vnonbon total external). Nonbonded energy and total potential energy are self explaining.
Example:
ANALYZE 137 158;
BELL (UINT)Niter
(UINT)FirstAtom (UINT)LastAtom
Iterative distance geometry optimizer using the Bellman  Ford  Fulkerson algorithm.
Parameters:  
Niter  Number of iterations. If it's less then 1, one iteration only is performed.  
FirstAtom  First atom serial for selection.  
LastAtom  Last atom serial for selection. This is an optional argument. If it's omitted, the LastAtom is the last atom in the molecule. 
Return message:
Build steps.
Example:
BELL 20 1;
See also:
ABUILD, DGEOM, GSDG,
KOHONEN.
BFGS (UINT)Niter
(UFLOAT)Toler
BFGS QuasiNewton minimizer. If the available memory isn't enough, the minimization is automatically switched to CNGDEL.
Parameters:  
Niter  Number of iterations.  
Toler  Tolerance value. 
Return message:
Minimization steps.
Example:
BFGS 100 1;
See also:
CNGDEL, GENETIC,
POLYTOPE, RIGID, STEEP,
TRUST.
Copy the current coordinate set and the active atom flag to the memory.
Parameters:  
CloneID  Identification number of the cloned coordinate set. It must be a positive number. 
Return message:
None.
Example:
CLONE 1;
CNGDEL 100 0 0.01;
RESTORE 1;
It clones the current coordinate set, performs an energy minimization and, finally, restores the coordinate set from the clone ID 1. In this way, the energy minimization is performed without changing the starting atomic coordinates.
See also:
RESTORE.
CNGDEL (UINT)Niter
(UINT)Nreset (UFLOAT)Toler
AMMP uses the PoliakRibeire algorithm for conjugate gradients with an inexact line search. AMMP will only terminate conjugate gradients when the number of steps is exhausted, or the calculated gradients are not a descent direction.
Parameters:  
Niter  Number of iterations.  
Nreset  Number of iterations resetting to steepest descent (STEEP).  
Toler  It's the desired value of the l_inifinity norm for the force. 
Return message:
During the iterations, AMMP prints the current potential, the l_inifinity norm
on the force, and the value of b which is the conjugate dot product. The
value for l_infinity will hop around as it is the magnitude of the maximum force
on any atom which can both increase and decrease.
The RMS force can be found by examining the value of the variable l2f (nop l2f;
or dump variable) which is the sum of the squares of the forces.
Example:
CNGDEL 100 0 0.01;
See also:
BFGS, GENETIC,
POLYTOPE, RIGID, STEEP,
TRUST.
DGEOM (UINT)Nstep
(UINT)Origin (FLOAT)Shift
Standard distance geometry optimizer implemented with the power method.
Parameters:  
Nstep  Number of steps. If it's less then 1, one iteration only is performed.  
Origin  It's the atom serial used as the key atom.  
Shift  Amount of eigenvalue shift. 
Return message:
Build steps.
Example:
DGEOM 20 1 0.5;
See also:
ABUILD, BELL, GSDG,
KOHONEN.
DIPOLE
(UINT)FirstAtom (UINT)LastAtom
Calculate the dipole moment.
Parameters:  
FirstAtom  First atom serial for selection.  
LastAtom  Last atom serial for selection. This is an optional argument. If it's omitted, LastAtom is the last atom in the molecule. 
Return message:
Dipole moment:
Dipole warning, 1 10 sum charge is not zero 1.000002 Dipole 1 10 center of charge is 0.237469 0.059340 0.008954
Example:
DIPOLE 1;
See also:
MONITOR.
DOUBLETIME
(UINT)Nstep
(UFLOAT)Dlong (UFLOAT)Dshort (UFLOAT)Temper
Double the time scale in molecular dynamics, performing a non linear fit and extrapolation.
Parameters:  
Nstep  Number of iterations.  
Dlong  Time scale.  
Dshort  Time step in m/s (0.00001 for 1 fs time integration).  
Temper  Temperature in Kelvin (default 300K). 
Return message:
MD steps.
Example:
DOUBLETIME 1000 2 0.00001
300;
See also:
HPAC, PAC, PACPAC,
PPAC, PTPAC, RICHARD,
TPAC,
V_MAXWELL, V_RESCALE,
VERLET.
DSCF
(CHAR)What
(UINT)Niter (UFLOAT)Toler
Direct SCF orbital optimizer.
Parameters:  
What  It could be: ANA (report only), CHARGE, COEF (coefficients), EDMAP, EMPIR, EXPO (exponents), FRE (freeze), GAN (gang toghether), GEOM (orbital geometry), IGEOM, INDO, IPOLI, PHIMAP, POLI, THA (thaw), XYZ (atom center).  
Niter 


Toler  Tolerance value. 
Return message:
Optimization step.
Example:
None.
GDOCK (UFLOAT)Toler
(UINT)Ndeep (UINT)Niter (FLOAT)VarA
(FLOAT)VarX (UINT)FirstAtom
(UINT)LastAtom
Genetic algorithm rigid docking. The specified atom range is docked into the rest of the structure.
Parameters:  
Toler  It's the desired value of the l_inifinity norm for the force.  
Ndeep  Number of possible solutions (population). In the initialization phase of the genetic algorithm the starting population is generated rototranslating randomly the selected atoms using the VarA and VarX scale factors. The default value is 8.  
Niter  Number of iterations (default 1).  
VarA  Rotation scale factor used to generate the starting population (default 1.0).  
VarX  Translation scale factor used to generate the starting population (default 1.0).  
FirstAtom  First atom number (not serial) of the selection (default 1).  
LastAtom  Last atom number (not serial) of the selection (default last atom). 
Return message:
Calculation steps steps.
Example:
GDOCK 1 10 100 1.0 1.0 145;
See also:
None.
GENETIC (UINT)Niter
(UINT)Ndeep (FLOAT)Sigma
(FLOAT)Target (UINT)NoptSteps
Genetic algorithm minimizer.
Parameters:  
Niter  Number of iterations.  
Ndeep  Number of possible solutions (population). In the initialization phase of the genetic algorithm the start population is randomly generated using the starting coordinates adding a random number (from 0 to 1) multiplied by the Sigma scale factor.  
Sigma  Scale factor used to generate the starting population.  
Target  When the population satisfies the Target value, the minimization is stopped.  
NoptSteps  Optimization steps with conjugate gradients method. (CNGDEL). 
Return message:
Minimization steps.
Example:
GENETIC 1000 10 1.0 0.01
10;
See also:
BFGS, CNGDEL,
POLYTOPE, RIGID, STEEP,
TRUST.
GRASP (UINT)Niter
(UINT)NoptSteps (UINT)FirstAtom
(UINT)LastAtom (CHAR)Atom
Torsion space optimizer. It searches a space of torsions using the current potentials and greedy algorithms. At least four atoms are required in the selection range (FirstAtom  LastAtom).
Parameters:  
Niter  Number of iterations.  
NoptSteps  Optimization steps with conjugate gradients method. (CNGDEL).  
FirstAtom  First atom number (not serial) for selection (optional, default = first atom).  
LastAtom  Last atom number (not serial) for selection (optional, default = last atom).  
Atom  Atom name in the atom selection (optional). 
Return message:
Minimization steps.
Example:
GRASP 100 10 1 100
c;
See also:
None.
GSDG (UINT)Niter
(UINT)FirstAtom (UINT)LastAtom
GSDG or GaussSiedel Distance Geometry is a hybrid Krylov solver for distance
geometry. It's related to the earlier Herman's minimizer used in programs like
FRODO and CHAIN, but is more robust and has a stronger theoretical background.
GSDG understands bond, angle, nonbon, and noel
potentials. It can work on any combination of these terms. It systematically,
one atom at a time, attempts to solve the distance equations. The nonbonded
exclusion target is set to 4.5 Ångstroms. This is too large and results in a
distorted structure when the nonbonded terms are used. However this distorted
structure is usually selfavoiding and readily corrected with conjugate
gradients (CNGDEL) to result in a structure with both good
geometry and selfavoidance.
GSDG is most useful for building simple small molecules, and adding moderate
sized chucks to a partial structure.
Only the number of cycles is required in which case all active atoms are
searched. If only one atom is specified then only it is searched. Otherwise the
range of atoms specified is searched. GSDG checks the atom range order and it
swap its terms if FirstAtom is greater than LastAtom.
Parameters:  
Niter  Number of iterations. If it's less then 1, one iteration only is performed.  
FirstAtom  First atom serial for selection (optional, default = first atom).  
LastAtom  Last atom serial for selection (optional, default = last atom). 
Return message:
Build steps.
Example:
GSDG 50;
See also:
ABUILD,
BELL, DGEOM.
HPAC (UINT)Nstep
(FLOAT)Dtime (FLOAT)Energy
Total energy constrained molecular dynamics, performing Nstep PAC dynamics.
Parameters:  
Nstep  Number of steps.  
Dtime  Time step in m/s (0.00001 for 1 fs time integration).  
Energy  Kinetic energy. 
Return message:
None.
Example:
HPAC 1000
0.00001 80.0;
See also:
DOUBLETIME, PAC, PACPAC,
PPAC, PTPAC, RICHARD,
TPAC,
V_MAXWELL, V_RESCALE,
VERLET.
INACTIVE
(UINT)FirstAtom (UINT)LastAtom
Inactivate the atoms for the next calculations. The inactive atoms aren't considered and they are kept fixed.
Parameters:  
FirstAtom  First atom serial for selection.  
LastAtom  Last atom serial for selection. This is an optional argument. If it's omitted, LastAtom is the last atom in the molecule. 
Return message:
None.
Example:
INACTIVE 34 132;
See also:
ACTIVE, NZINACTIVE.
KOHONEN (UINT)Niter
(UFLOAT)Radius (INT)Initialize (UFLOAT)Rx (UFLOAT)Ry (UFLOAT)Rz
Kohonen neural network to find the 3D space filling curve corresponding to the structure: the net links correspond to chemical bonds, angle distances, noel distances and eventually the distance update could also include the Van der Waals interactions and the chirality. The Kohonen algorithm implements a selforganizing neural network that possess an isometry with selfassembling physical systems. One particular system of interest is proteins and other polymers.
Parameters:  
Niter  Number of iterations.  
Radius  It's the sphere radius in Å used to initialize the starting coordinates (see Initialize). If it's a value less then 1.0 Å, it's automatically computed as square root of the number of atoms.  
Initialize  If it's 1, the neural network is initialized assigning
random coordinates for each active atom. The inactive atoms, if they are
present, are used to calculate the geometry centre of the molecule. If no
inactive atoms are available, the geometry centre is placed at 0, 0, 0. The
random coordinates are scaled to Radius in order to fill completely
the sphere that will contain the final structure. If the Initialize value is 1, the neural network isn't initialized and it continues the previous calculation. 

Rx  Symmetry radii in Å:
The cylindrical and ellipsoidal symmetries ignore the Radius value, and the spherical symmetry uses Radius value. 

Ry  
Rz 
Return message:
Build steps.
Example:
KOHONEN 100 1 1
0.0;
See also:
ABUILD,
BELL, DGEOM, GSDG.
MOM
(FLOAT)TotalCharge (UINT)Niter
Perform the MoM atomic charge calculation. The algorithm is based on the moments developed by Rappe and Goddard. The atoms must be selected with the MOMADD command before to start the MoM calculation.
Parameters:  
TotalCharge  Molecule total charge.  
Niter  Number of iterations. If it's less then 0, the default number of iterations is performed (20). 
Return message:
Charge attribution steps with error value:
MoM : Initialization MoM 4: Error 1.440886e01 MoM 8: Error 1.476538e02
Example:
MOM 1.0 20;
MOMADD
(UINT)FirstAtom (UINT)LastAtom
Select the atoms for the MoM calculation. It can be called
more then one time and the selection is lost when MOM is
executed.
Parameters:  
FirstAtom  First atom serial for selection.  
LastAtom  Last atom serial for selection. This is an optional argument. If it's omitted, LastAtom is the last atom in the molecule. 
Return message:
None.
Example:
MOMADD 1 100;
Perform a single point energy evaluation. The USE command allows to select the energies to dump.
Parameters:
None.
Return message:
Dump of energies in Kcal/mol:
Energy: Bond................: 1.080161 Angle...............: 2.006297 Torsion.............: 7.762559 Nonbond............: 10.683147 Hybrid..............: 1.009054 Total potential.....: 22.541220 Total kinetic.......: 0.000000 Total energy........: 22.541220 Total action........: 22.541220
Example:
MONITOR;
See also:
DIPOLE,
USE.
Calculate the normal modes. This is useful for small molecules.
Parameters:  
Damp  Normal scale factor. If it's equal to 0, the eigenvalues are dumped only. If it's greater then 0, the structures are dumped in PDB multimodel format. The resulting file (see output command) is readable by VEGA ZZ or by other molecular modelling software supporting the PDB multimodel format. 
Return message:
The computed Eigenvalues if Damp is less or equal to 0:
81 Eigenvalues found: 414.515198 kcal/A^2g 3126.659427 cm1 412.284485 kcal/A^2g 3118.235021 cm1 401.209595 kcal/A^2g 3076.068513 cm1 400.785583 kcal/A^2g 3074.442639 cm1 400.264404 kcal/A^2g 3072.442995 cm1
Example:
NORMAL 0;
See also:
None.
NZINACTIVE
(UINT)FirstAtom (UINT)LastAtom
Inactivate the atoms which aren't located at the axis origin (0, 0, 0). The inactive atoms aren't considered and they are kept fixed.
Parameters:  
FirstAtom  First atom serial for selection.  
LastAtom  Last atom serial for selection. This is an optional argument. If it's omitted, LastAtom is the last atom in the molecule. 
Return message:
None.
Example:
NZINACTIVE 20 78;
Perform the molecular dynamics, predicting the path given current velocity, integrating the force (Simpson's rule), predicting the final velocity and updating the position using trapezoidal correction.
Parameters:  
Nstep  Number of steps (default 1).  
Dtime  Time step in m/s (0.00001 for 1 fs time integration).The default value is 0.00001. 
Return message:
None.
Example:
PAC 1000
0.00001;
See also:
DOUBLETIME, HPAC,
PACPAC, PPAC,
PTPAC, RICHARD, TPAC, V_MAXWELL,
V_RESCALE, VERLET.
PACPAC (UINT)Nstep
(FLOAT)Dtime
Perform the molecular dynamics, predicting the path given current velocity, integrating the force (Simpson's rule), predicting the final velocity and updating the position using trapezoidal correction. This is the more accurate version of PAC.
Parameters:  
Nstep  Number of steps (default 1).  
Dtime  Time step in m/s (0.00001 for 1 fs time integration). The default value is 0.00001. 
Return message:
None.
Example:
PACPAC 1000
0.00001;
See also:
DOUBLETIME, HPAC, PAC,
PPAC,
PTPAC, RICHARD, TPAC, V_MAXWELL,
V_RESCALE, VERLET.
POLYTOPE
(UINT)FirstAtom (UINT)LastAtom (UINT)Niter
(UFLOAT)Vstart (UFLOAT)Vfinal
Perform a polytope simplex minimization on a selected range of atoms.
Parameters:  
FirstAtom  First atom serial for selection.  
LastAtom  Last atom serial for selection. If it's set to 0, LastAtom is the last atom in the molecule.  
Niter  Number of iterations.  
Vstart  Starting variance. It's the scale factor used to move the atom coordinates.  
Vfinal  Target (final) variance. 
Return message:
Minimization steps.
Example:
POLYTOPE 1 0 100
0.5 0.01;
See also:
BFGS, CNGDEL, GENETIC,
RIGID, STEEP, TRUST.
PPAC (UINT)Nstep
(FLOAT)Dtime (UFLOAT)Press
Pressure constrained molecular dynamics. The volumes are not fully calibrated in this command. It is also necessary to slowly approach the desired conditions because this uses Andersen's demon for volume constraints. Andersen's demon is not fully stable and the system can explode.
Parameters:  
Nstep  Number of steps (default 1).  
Dtime  Time step in m/s (0.00001 for 1 fs time integration).The default value is 0.00001.  
Press  Pressure in kilopascal (101.325 kPa = 1.0 atm). 
Return message:
None.
Example:
PPAC 1000
0.00001 101.325;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PTAC,
RICHARD, TPAC, V_MAXWELL,
V_RESCALE, VERLET.
PTPAC (UINT)Nstep
(FLOAT)Dtime (UFLOAT)Temp
(UFLOAT)Press
Temperature and pressure constrained molecular dynamics. The volumes are not
fully calibrated in this command. It is also necessary to slowly approach the
desired conditions because this uses Andersen's demon for volume constraints.
Andersen's demon is not fully stable and the system can explode.
Parameters:  
Nstep  Number of steps (default 1).  
Dtime  Time step in m/s (0.00001 for 1 fs time integration).The default value is 0.00001.  
Temp  Temperature in Kelvin.  
Press  Pressure in kilopascal (101.325 kPa = 1.0 atm). 
Return message:
None.
Example:
PTPAC 1000
0.00001 310 101.325;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PPAC,
RICHARD, TPAC, V_MAXWELL,
V_RESCALE, VERLET.
Copy a coordinate set and the active atom flag from the memory.
Parameters:  
CloneID  Identification number of the cloned coordinate set. It must be a positive number. 
Return message:
If the clone ID is not available, an error message is shown.
Example:
RESTORE 1;
See also:
CLONE.
RICHARD
(CHAR)Who (UINT)Nstep
(FLOAT)MDparam1 (FLOAT)MDparam2 (FLOAT)MDparam3
Thermodynamic path integrals using the Feynmann Weiner Kac approach (Wiener version).
Parameters:  
Who  Clculation type. It could be: PAC, PACPAC, TPAC, HPAC, PTPAC, VERLET.  
Nstep  Number of steps (default 1).  
MDparam1  Optional parameters required by the specified calculation type. For more information, see the appropriate command section.  
MDparam2  
MDparam3 
Return message:
None.
Example:
RICHARD PAC 1000
0.00001;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PPAC,
PTPAC, TPAC, V_MAXWELL,
V_RESCALE, VERLET.
RIGID (UINT)FirstAtom
(UINT)LastAtom (UINT)Niter
(UFLOAT)Vstart (UFLOAT)Vfinal
Polytope rigidbody optimization.
Parameters:  
FirstAtom  First atom serial for selection.  
LastAtom  Last atom serial for selection. If it's set to 0, LastAtom is the last atom in the molecule.  
Niter  Number of iterations.  
Vstart  Starting variance. It's the scale factor used to move the atom coordinates.  
Vfinal  Target (final) variance. 
Return message:
Optimization steps.
Example:
RIGID 1 0 100 0.5
0.01;
See also:
BFGS, CNGDEL, GENETIC,
POLYTOPE, STEEP,
TRUST.
STEEP (UINT)Niter
(UFLOAT)Toler
Steepest descent minimizer. If it's unable to satisfy the Toler value,
the minimization is automatically stopped.
Parameters:  
Niter  Number of iterations.  
Toler  It's the desired value of the l_inifinity norm for the force. 
Return message:
During the iterations, AMMP prints the current potential, the l_inifinity norm
on the force. The
value for l_infinity will hop around as it is the magnitude of the maximum force
on any atom which can both increase and decrease.
Example:
STEEP 100 1;
See also:
BFGS, CNGDEL, GENETIC,
POLYTOPE, RIGID, TRUST.
TGROUP (UINT)Id
(UINT)Atom1 (UINT)Atom2
(UINT)Atom3 (UINT)Atom4
(UFLOAT)Base (UINT)Steps
(UFLOAT)TorWin
Define a torsion for the conformational search.
Parameters:  
Id  Torsion identification number. It must be greater then 0.  
Atom1  Atom serials defining the torsion.  
Atom2  
Atom3  
Atom4  
Base  Base torsion value in degree (default 0°). It must be in the 0  360° range.  
Steps  Number of search steps (default 6) used in the systematic conformational search (TSEARCH).  
TorWin  Torsion window value in degree (default 360°) used in the random search. It must be in the 0  360° range. It causes a random rotation on the torsion in the range from 0 to its value during the Boltzmann jump and random conformational search (TJUMP, TRANDOM). When you perform a systematic conformational search (TSEARCH), this is the ending value assumed during the scan. 
Return message:
Error message if an illegal parameter is present.
Example:
TGROUP 1
7 12 13 14 0.0 6
30.0;
See also:
TJUMP, TRANDOM, TSEARCH.
TJUMP (UINT)Niter
(UINT)MinIter
(UFLOAT)MinToler (UFLOAT)Temp (UFLOAT)Rmsd
Perform the Boltzmann jump conformational search rotating randomly
the active torsions. The amplitude of the torsion changes is defined by the torsion window
values (see TGROUP command). Base value defined
by TGROUP is ignored and so the random perturbation is done starting from the
original conformation. The number of the
torsions that can be used to generate the conformations is unlimited. At
the end of the conformational search, the memory contains the best conformation
found.
The Boltzmann jump method allows upward energy jumps: if the potential of the
new random generated conformer is lower than the previous one, it will be
selected as reference conformation, but if the potential is higher than the
previous one, a stochastic decision is requested. The probability of selecting
the new conformation is equal to the Boltzmann factor:
F = e^{ΔE/RT}
where ΔE is the potential difference between the two
conformers, R is the gas constant (1.987 cal · K^{1} · mol ^{
1}) and T is the temperature in Kelvin. A random number N
is generated in the range from 0 to 1 and if N > F, the conformation is
selected, otherwise (N < F) the conformation is rejected. The chances of
making an upward jump in energy are greater at a higher temperature (T)
or at a smaller energy difference (E).
The starting conformation undergoes a thermal perturbation in which the selected
torsion are randomly rotated and if the resulting conformation is of lower
energy, that's selected. If the perturbed conformation is of higher energy, the
stochastic decision is requested, as explained above, to select or reject the
new conformation. The random perturbation is carried out until the root mean
square deviation (RMSD) between the reference and the new conformation exceeds
the specified maximum RMSD value. When this condition is reached, the conjugate
gradients minimization is performed and the resulting conformation is selected
as new reference.
If the Boltzmann jump parameters are wrong, it's possible that the condition to
exit from the perturbation phase is never reached. To avoid this problem, the
MxPerIter variable sets the maximum number
of perturbation iteration over which the procedure is stopped and the generated
conformation is minimized.
Parameters:  
Niter  Number of random conformation that will be generated.  
MinIter  Number of conjugate gradients minimization steps.  
MinToler  It's the desired value of the l_inifinity norm for the force.  
Temp  Temperature in Kelvin (default 300 K).  
Rmsd  Root mean square difference (RMSD) value between the reference and the perturbed conformation over them the energy minimization is performed (default 60.0 degrees). 
Return message:
AMMP shows the random search steps:
Starting Boltzmann jump search (100 steps, 2000.0 K, 60.00 perturbation RMSD)
Tjump 1: ps 1, vb 111.135, v 174.606, vmin 117.072 Tjump 2: ps 5, vb 111.135, v 64992120832.000, vmin 115.894 Tjump 3: ps 1, vb 111.135, v 4584.223, vmin 114.690 Tjump 4: ps 1, vb 111.135, v 688399360.000, vmin 113.482 Tjump 5: ps 8, vb 111.135, v 275.485, vmin 119.162 Tjump 6: ps 1, vb 111.135, v 1170.165, vmin 126.796 Tjump 7: ps 1, vb 111.135, v 1498841.500, vmin 122.223 Tjump 8: ps 1, vb 111.135, v 34582256.000, vmin 121.838 Tjump 9: ps 3, vb 111.135, v 161768.172, vmin 117.854 Tjump 10: ps 1, vb 111.135, v 8072.150, vmin 116.928 Tjump 11: ps 1, vb 111.135, v 573.954, vmin 125.318 ...
Best conformation selected (v 93.904305)
In each line is shown: the conformational search step, the
number of conformations generated during the thermal perturbation phase (ps),
the lowest potential found (vb), the
potential (v), and the
potential of the minimized conformer (vmin). This last value is not shown
if the conformer minimization is not performed or disabled (see the MinIter parameter).
The last line informs that the best conformer found is selected (its coordinates
are available in memory) and it shows its potential (v).
Example:
TJUMP 3000
20 0.0 500;
See also:
TGROUP, TMIN,
TRANDOM,
TSEARCH.
TMAP
(UINT)I1
(UINT)I2 (UINT)I3
(UINT)I4
(UINT)J1
(UINT)J2 (UINT)J3
(UINT)J4
(UINT)Isteps (UINT)Jsteps
Map two torsions rotating them systematically. It requires at least five atoms.
Parameters:  
I1  Atom serials defining the first torsion.  
I2  
I3  
I4  
J1  Atom serials defining the second torsion.  
J2  
J3  
J4  
Isteps  Number of search steps for the first torsion (default 12).  
Jsteps  Number of search steps for the second torsion (default 12). 
Return message:
None.
Example:
TMAP 7
12 13 14 12 13 14
15 20 20;
See also:
TJUMP,
TMIN, TRANDOM,
TSEARCH, TSET.
TMIN
(UINT)Atom1
(UINT)Atom2 (UINT)Atom3
(UINT)Atom4 (UINT)Steps
Minimize a torsion systematically rotating it.
Parameters:  
Atom1  Atom serials defining the torsion.  
Atom2  
Atom3  
Atom4  
Steps  Number of search steps (default 12). 
Return message:
Show the torsion search steps and the final torsion value:
Starting the torsion minimizer (angle 91.845, steps 24) Tmin 1: angle 15.000, v 41.004, vb 41.004 Tmin 11: angle 165.000, v 28.959, vb 22.675 Tmin 21: angle 315.000, v 24.826, vb 22.675 Tmin 24: angle 360.000, v 34.080, vb 22.675 Best conformation selected (angle 105.000, v 22.674868)
Example:
TMIN 7
12 13 14 24;
See also:
TGROUP, TJUMP, TMAP,
TRANDOM,
TSEARCH, TSET.
TPAC (UINT)Nstep
(FLOAT)Dtime (UFLOAT)Temp
Temperature constrained molecular dynamics.
Parameters:  
Nstep  Number of steps (default 1).  
Dtime  Time step in m/s (0.00001 for 1 fs time integration).The default value is 0.00001.  
Temp  Temperature in Kelvin. 
Return message:
None.
Example:
TPAC 1000
0.00001 300;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PPAC,
PTPAC, RICHARD, V_MAXWELL,
V_RESCALE, VERLET.
TSET
(UINT)Atom1
(UINT)Atom2 (UINT)Atom3
(UINT)Atom4 (FLOAT)TorVal
Set the torsion angle.
Parameters:  
Atom1  Atom serials defining the torsion.  
Atom2  
Atom3  
Atom4  
TorVal  New torsion value in degree. 
Return message:
The new torsion value:
Tset : Original 91.845497, delta 88.154503, final 180.000000
Example:
TSET 7
12 13 14 180.0;
See also:
TGROUP, TJUMP, TMAP, TMIN,
TRANDOM, TSEARCH.
TRUNC (UINT)Niter
(UFLOAT)Dtoler (UFLOAT)Toler
Truncated Newton method minimizer. It's based on the idea that an exact solution of the Newton equation at every step is unnecessary and can be computationally wasteful in the framework of a basic descent method. Any descent direction will suffice when the objective function is not well approximated by a convex quadratic and, as a solution to the minimization problem is approached, more effort in solution of the Newton equation may be warranted. Their appeal to scientific applications is their ability to exploit function structure to accelerate convergence.
Parameters:  
Niter  Number of iterations.  
Dtoler  Approximation to truncate the Newton equation. The default value is 0.001 and values less then 0.001 aren't allowed, resetting automatically to the default.  
Toler  It's the desired value of the l_inifinity norm for the force. 
Return message:
During the iterations, AMMP prints the current potential, the l_inifinity norm
on the force, and the value of b which is the conjugate dot product. The
value for l_infinity will hop around as it is the magnitude of the maximum force
on any atom which can both increase and decrease.
The RMS force can be found by examining the value of the variable l2f (nop l2f;
or dump variable) which is the sum of the squares of the forces.
Example:
TRUST 3000 0.001 0.01;
See also:
BFGS, CNGDEL, GENETIC,
POLYTOPE, RIGID, STEEP,
TRUST.
TRUST (UINT)Niter
(UFLOAT)Dtoler (UFLOAT)Toler
Trustregion based minimizer. If it's unable to satisfy the Toler value, the minimization is automatically stopped. The theory is to move in a steepest descent direction until the disagreement between observed and calculated energies is too high.
Parameters:  
Niter  Number of iterations.  
Dtoler  Disagreement value between observed and calculated energies. The default value is 0.1 and values less then 0.001 aren't allowed, resetting automatically to the default.  
Toler  It's the desired value of the l_inifinity norm for the force. 
Return message:
During the iterations, AMMP prints the current potential, the l_inifinity norm
on the force. The
value for l_infinity will hop around as it is the magnitude of the maximum force
on any atom which can both increase and decrease.
Example:
TRUST 1000 0.1 1.0;
See also:
BFGS, CNGDEL, GENETIC,
POLYTOPE, RIGID, STEEP.
TRANDOM (UINT)Niter
(UINT)MinIter
(UFLOAT)MinToler (BOOL)KeepPrev (BOOL)KeepMin
Perform the random conformational search rotating randomly the active torsions. The torsion starting value and the torsion windows are set by the TGROUP command. The torsion window is The number of the torsions that can be used to generate the conformations is unlimited. At the end of the conformational search, the memory contains the best conformation found.
Parameters:  
Niter  Number of random conformation that will be generated.  
MinIter  Number of conjugate gradients minimization steps performed for each conformation rotating systematically the active torsions defined by the TGROUP command. If it's zero, the minimization is not performed and the singlepoint energy is evaluated to choose the best rough conformation.  
MinToler  It's the desired value of the l_inifinity norm for the force.  
KeepPrev  If it's true (1), the random modifications are applied to the previous nonminimized conformation (default false, 0).  
KeepMin  If it's true (1) and MinIter is greater than zero, the random modifications are applied to the previous minimized conformation (default false, 0). 
Return message:
AMMP shows the random search steps:
Starting random conformational search (100 steps)
Trandom 1: v 14123088896.000, vb 14123088896.000, vmin 113.733 Trandom 2: v 18819.949, vb 113.733, vmin 107.588 Trandom 3: v 307.890, vb 107.588, vmin 114.008 Trandom 4: v 136.162, vb 107.588, vmin 112.244 Trandom 5: v 17879676928.000, vb 107.588, vmin 118.615 Trandom 6: v 18261741568.000, vb 107.588, vmin 127.483 Trandom 7: v 161.983, vb 107.588, vmin 113.163 Trandom 8: v 685030.000, vb 107.588, vmin 109.987 Trandom 9: v 30623124.000, vb 107.588, vmin 1561.937 Trandom 10: v 159.711, vb 107.588, vmin 108.041 ... Best conformation selected (v 101.695412)
In each line is reported: the conformational search step, the
potential (v), the best potential found at that step (vb) and the
potential of the minimized conformer (vmin). This last value is not shown
if the conformer minimization is disabled (see the MinIter parameter).
The last line informs that the best conformer found is selected (its coordinates
are available in memory) and it shows its potential (v).
Example:
TRANDOM 1000
20 0.0 0 0;
See also:
TGROUP, TMIN,
TSEARCH.
TSEARCH (UINT)MinIter
(UFLOAT)MinToler
Perform the systematic conformational search (grid scan) rotating systematically the active torsions. The torsion starting value and the number of rotation steps are set by the TGROUP command. The number of the torsions that can be used to generate the conformations is unlimited. At the end of the conformational search, the memory contains the best conformation found.
Parameters:  
MinIter  Number of conjugate gradients minimization steps performed for each conformation rotating systematically the active torsions defined by the TGROUP command. If it's zero, the minimization is not performed and the singlepoint energy is evaluated to choose the best rough conformation.  
MinToler  It's the desired value of the l_inifinity norm for the force. 
Return message:
AMMP shows the torsion search steps:
Starting systematic conformational search (6 steps)
Tsearch 1: v 142.206, vb 142.206, vmin 107.684 Tsearch 2: v 134.114, vb 107.684, vmin 108.797 Tsearch 3: v 138.397, vb 107.684, vmin 107.635 Tsearch 4: v 135.108, vb 107.635, vmin 111.325 Tsearch 5: v 141.933, vb 107.635, vmin 110.274 Tsearch 6: v 136.650, vb 107.635, vmin 106.573
Best conformation selected (v 106.573456)
In each line is reported: the conformational search step, the
potential (v), the best potential found at that step (vb) and the
potential of the minimized conformer (vmin). This last value is not shown
if the conformer minimization is disabled (see the MinIter parameter).
The last line informs that the best conformer found is selected (its coordinates
are available in memory) and it shows its potential (v).
Example:
TSEARCH 20
0.0;
See also:
TGROUP, TMIN,
TRANDOM.
Select the force field terms for energy calculation. By the same command, you can select more then one term.
Parameters:  
FFTerm 
Force field term. It could be:

Return message:
None.
Example:
USE none
bond angle torsion;
See also:
BFGS, CNGDEL, GENETIC,
POLYTOPE, RIGID, STEEP,
TRUST.
V_MAXWELL
(UFLOAT)Temp
(FLOAT)Dx (FLOAT)Dy
(FLOAT)Dz
Set the velocity distribution with a random Maxwell  Boltzmann distribution.
Parameters:  
Temp  Temperature in Kelvin.  
Dx  Starting velocity along the X axis (optional value, default 0).  
Dy  Starting velocity along the Y axis (optional value, default 0).  
Dz  Starting velocity along the Z axis (optional value, default 0). 
Return message:
None.
Example:
V_MAXWELL
300.0;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PPAC,
PTPAC, RICHARD, TPAC, V_RESCALE,
VERLET.
Rescale the velocities to a new temperature.
Parameters:  
Temp  Temperature in Kelvin. 
Return message:
None.
Example:
V_RESCALE
300;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PPAC,
PTPAC, RICHARD, TPAC, V_MAXWELL,
VERLET.
VERLET
(UINT)Nstep
(UFLOAT)Dtime
Perform the leapfrogging molecular dynamics. This is here for historical reasons and is occasionally useful.
Parameters:  
Nstep  Number of steps (default 1).  
Dtime  Time step in m/s (0.00001 for 1 fs time integration).The default value is 0.00001. 
Return message:
None.
Example:
VERLET 1000
0.00001;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PPAC,
PTPAC, RICHARD, TPAC, V_MAXWELL,
V_RESCALE.