# Create terminally-blocked alanine peptide model with AMBER ff96 and OBC GBSA.

# Load AMBER '96 forcefield for protein.
source leaprc.ff96

# Create sequence.
peptide = sequence { ACE ALA NME }

# Check peptide.
check peptide

# Report on net charge.
charge peptide

# Solvate in water box.
solvateBox peptide TIP3PBOX 9.0 iso

# Write parameters.
saveAmberParm peptide alanine-dipeptide.prmtop alanine-dipeptide.crd

# Exit
quit