Minimizing the Potential Energy



# Read the full peptide structure (after linking and building);
echo off;
read peptide.all.ammp;
echo on;

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

setf mxdq 1.0;

# Activate all atoms;
active 0 1000000;

# Use just non-bonded term for potential energy function;
# Perform 100 conjugate gradient iterations on the potential energy;

use none bond;
cngdel 100;

# Add angle term and perform 100 conjugate gradient iterations;
use angle;
cngdel 100;

# Add hybrid term and perform 50 conjugate gradient iterations;
use hybrid;
cngdel 50;

# Add torsion and non-bonded terms and perform 100 iterations;
use torsion nonbon;
cngdel 100;

# Use bond, angle, hybrid, torsion, and non-bonded terms;
# Perform 200 conjugate gradient iterations on the potential energy;

use none bond angle hybrid torsion nonbon;
cngdel 200;

# Ouput new ammp and pdb files;
echo off;
output peptide.min.ammp;
dump atom bond angle hybrid restrain torsion nonbon; close;
output peptide.min.pdb; dump pdb; close;
exit;