# 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;