Creating Peptide Bonds

Creating Peptide Bonds



# read the peptide structure information;
echo off;
read peptide.ammp;

# loop from residue 1 to 10;
seti ires 1;
loopi end: ires 11;
mov jres ires;
add jres 1;

# read peplink file to define peptide bond;
echo off;
read peplink.ammp; # AMMP script to define peptide bonds;
echo on;
end:; # label designating end of loop;

# output an ammp file containing the new bonding terms;
echo off;
output peptide.link.ammp;
dump atom bond angle hybrid torsion; close;
exit;