tleap_script.txt

#Load Amberff14sb and TIP3P waters
source leaprc.protein.ff14SB
source leaprc.water.tip3p

#Load Amber prepi files for the fluorinated proline residues
loadamberprep ./tleap_prep/rf.prepin
loadamberprep ./tleap_prep/sf.prepin

# Load gaff2 for bond, angle and dihedrals containing fluorine
# Load vdw parameters for F and Hf (H bonded to fluorinated carbon) - Robalo et al. Phys. Chem. Chem. Phys., 2019,21, 2029-2038
loadamberparams ./tleap_prep/F.frcmod

#####################################################################
# User can choose the peptide to simulate below 
#####################################################################
#Example 1 (Simple 4R fluorinated Proline dipeptide) (RF in short)
amber=sequence{ACE PRF NME}
 
#Example 2 (Simple 4S fluorinated Proline dipeptide) (SF in short)
#amber=sequence{ACE PSF NME}

#Example 3 (Tetrapeptide)
#amber=sequence{ACE PRF PRF PSF NME}
#####################################################################

#Add waters 
solvatebox amber TIP3PBOX 10

#save pdb and amber topologies
savepdb amber amber_ff/amber.pdb
saveamberparm amber amber_ff/amber.prmtop amber_ff/amber.inpcrd

quit