Building New Atoms



# read the linked peptide structure;
echo off;
read peptide.link.ammp;
echo on;

# activate only atoms without coordinates;
nzinactive 0 100000000;

# use the bond, angle, hybrid, torsion, and non-bonded terms for the forcefield;
use none bond angle hybrid torsion nonbon;

# build new atoms using the 15 cycles of the gsdg algorithm;
gsdg 15 0 100000000;

# output an ammp file containing the new structure;
echo off;
output peptide.all.ammp;
dump atom bond angle hybrid torsion nonbon; close;
exit;