5. Examples

In this manual section are shown some examples explaining the AMMP use. You must remember that AMMP and VEGA ZZ packages include examples directory containing other examples.

5.1 Conjugate gradients minimization
5.2 Genetic algorithm minimization
5.3 Distance geometry optimizer
5.4 MoM charge calculation
5.5 Dipole moment evaluation
5.6 Genetic algorithm rigid docking
5.7 Evaluation of Interaction energy
5.8 Molecular dynamics

5.1 Conjugate gradients minimization

# Disable the command echo;

echo off;

# Set the atoms and the electronegativity terms;

atom -0.850184 -0.005877 -0.043286 1 unk.c 0.117245 26.171595 1056.904541 12.010700;
mompar 1 5.343000 10.126000;
atom -1.551700 0.980789 0.182142 2 unk.o -0.301327 14.852336 450.281281 15.999400;
mompar 2 8.241000 13.364000;
atom 0.637317 0.007546 0.033391 3 unk.c2 -0.009123 26.171595 1056.904541 12.010700;
mompar 3 5.343000 10.126000;
atom 0.979426 -0.740195 0.790381 4 unk.h23 0.030297 7.130669 121.200447 1.007900;
mompar 4 4.528000 13.890400;
atom -1.302962 -0.984543 -0.323522 5 unk.h 0.102314 7.130669 121.200447 1.007900;
mompar 5 4.528000 13.890400;
atom 1.065112 -0.273145 -0.960361 6 unk.h21 0.030297 7.130669 121.200447 1.007900;
mompar 6 4.528000 13.890400;
atom 1.022991 1.015424 0.321254 7 unk.h22 0.030297 7.130669 121.200447 1.007900;
mompar 7 4.528000 13.890400;

# Bonds;

bond 1 2 1.225000 640.000000;
bond 1 3 1.489000 289.684265;
bond 1 5 1.087000 314.000000;
bond 3 6 1.112599 352.394226;
bond 3 7 1.112599 352.394226;
bond 3 4 1.112599 352.394226;

# Angles;

angle 2 1 3 98.000000 121.900002;
angle 2 1 5 50.000000 124.500000;
angle 3 1 5 40.926056 120.000000;
angle 1 3 6 40.688461 109.470001;
angle 1 3 7 40.688461 109.470001;
angle 1 3 4 40.688461 109.470001;
angle 6 3 7 41.660091 109.470001;
angle 6 3 4 41.660091 109.470001;
angle 7 3 4 41.660091 109.470001;

# Torsion angles;

torsion 2 1 3 6 1.666667 3 180.000000;
torsion 2 1 3 7 1.666667 3 180.000000;
torsion 2 1 3 4 1.666667 3 180.000000;
torsion 5 1 3 6 1.666667 3 180.000000;
torsion 5 1 3 7 1.666667 3 180.000000;
torsion 5 1 3 4 1.666667 3 180.000000;

# Hybrids;

hybrid 2 3 5 1 150.000000 0.000000;
echo on;

# Set the force field terms;

use none bond angle torsion hybrid nonbon;

# Show the starting energy;

monitor;

# Update full non-bonded list when atomic displacement is
# greater than 1.0 angstroms;

setf mxdq 1.0;

# Start the minimization (2000 steps, toler 0.01);

cngdel 2000 0 0.01;

# Show the final energy;

monitor;

# Dump the final structure in AMMP and PDB formats;

echo off;
output molecule_min.pdb;
dump pdb;
close;

output molecule_min.amp;
dump atom bond;
close;
echo on;

5.2 Genetic algorithm minimization

# Read the molecule from another file;

echo off;
read molecule.amp;
echo on;

# Set the force field terms;

use none bond angle torsion nonbon;

# Update full non-bonded list when atomic displacement is
# greater than 1.0 angstroms;

setf mxdq 1.0;

# Start the minimization (1000 steps, population of 10 subjects, 1.0 sigma;
# scale factor for starting population generation, 0.01 target value;
# 10 minimization steps of conjugate gradients;

genetic 1000 10 1.0 0.01 10;

# Dump the final structure in AMMP format;
echo off;
output molecule_min.amp;
dump atom bond;
close;
echo on;

5.3 Distance geometry optimizer

# Read the molecule that have all atoms at;
# (0.0, 0.0, 0.0);

echo off;
read molecule.amp;
echo on;

# Start dgeom (20 steps, key atom 1, shift 0.5);
# It builds the molecule using the power method;

dgeom 20 1 0.5;

# Dump the final structure in PDB format;
echo off;
output molecule_min.pdb;
dump pdb;
close;
echo on;

5.4 MoM charge calculation

# Read the molecule;

echo off;
read molecule.amp;
echo on;

# Select the atoms (from 1 to last atom);

momadd 1;

# Start mom (20 steps, total charge +1.0);

mom 1.0 20;

# Dump the final charges in AMMP format;
echo off;
output molecule_out.amp;
dump atom;
close;
echo on;

5.5 Dipole moment evaluation

# Read the molecule;

echo off;
read molecule.amp;
echo on;

# Calculate the dipole moment (from 1 to last atom);

dipole 1;

5.6 Genetic algorithm rigid docking

# Read file containing the ligand and the target molecule;
# (e.g. receptor protein);

echo off;
read complex.amp;
echo on;

# Set the force field terms;

use none bond angle torsion nonbon;

# Update full non-bonded list when atomic displacement is
# greater than 1.0 angstroms;

setf mxdq 1.0;

# Start the docking (1.0 toler, 10 Ndeep, 100 iterations,;
# 1.0 VarA, 1.0 VarX, 145 first atom);

gdock 1.0 10 100 1.0 1.0 145;

# Dump the final structure in AMMP format;

echo off;
output complex_dock.amp;
dump atom bond;
close;
echo on;

5.7 Evaluation of Interaction energy

# Read the file containing the complex between the ligand and;
# the receptor;

echo off;
read molecule.amp;

# Set the force field terms;

use none nonbon;

# Update full non-bonded list when atomic displacement;
# greater than 0.75 angstroms;

setf mxdq 0.75;

# Enable the multipole algorithm;

setf mmbox 10.0;

# Start the analysis (the 9173 - 9231 atom range is the ligand);

echo on;
analyze 9173 9231;

# Vnonbond total external is the interaction energy;

5.8 Molecular dynamics

echo off;

# Set the number of steps (1 step = 1 ps);

seti steps 100; # 100 ps;

# Trajectory update (every 10 ps);

seti refresh 10;

# Read the molecule;

read molecule.amp;

# Set the force field terms;

use none bond angle torsion hybrid nonbon;

# Update full non-bonded list when atomic displacement;
# greater than 0.75 angstroms;

setf mxdq 0.75;

# Set the temperature to 300 Kelvin;

setf temp 300;

# Initialize atomic velocities with a boltzmann distribution;

v_maxwell temp;

# Check the energies prior to MD run;

echo on;
monitor;
echo off;

# Run the molecular dynamics;

seti n 0;
seti r 0;
div steps refresh;

echo off;
loopi end1: r steps;
  seti i 0;
  loopi end2: i refresh;
    tpac 1000 0.00001 temp;
    add n 1;
  end2:;

  echo on;
  nop n;
  monitor;
  echo off;

  # Save the frame;

  output molecule_md.amp n;
  dump atom bond angle hybrid torsion nonbon velocity;
  close;
end1:;