source leaprc.ff99
logFile LEaP-Tutorial-2.log

verbosity 2

AIB = loadmol2 5-Charges-2conf-RBRA-4-INTRA-MCC/Mol_m1-o1-sm.mol2
NAIB = loadmol2 6-Charges-2conf-RBRA-4-INTER-MCC1/Mol_MM1/Mol_m2-o1-mm1.mol2
CAIB = loadmol2 6-Charges-2conf-RBRA-4-INTER-MCC2/Mol_MM1/Mol_m2-o1-mm1.mol2

charge AIB
charge NAIB
charge CAIB

# set general information for AIB
set AIB name "AIB"
set AIB.1 restype protein
set AIB.1 name "AIB"
set AIB head AIB.1.N
set AIB tail AIB.1.C
set AIB.1 connect0 AIB.1.N
set AIB.1 connect1 AIB.1.C
# set FF atom types for AIB
set AIB.1.N type N
set AIB.1.H type H
set AIB.1.CA type CT
set AIB.1.CB1 type CT
set AIB.1.HB11 type HC
set AIB.1.HB12 type HC
set AIB.1.HB13 type HC
set AIB.1.CB2 type CT
set AIB.1.HB21 type HC
set AIB.1.HB22 type HC
set AIB.1.HB23 type HC
set AIB.1.C type C
set AIB.1.O type O
# save the OFF library for AIB
saveoff AIB AIB.off

# set general information for NAIB
set NAIB name "NAIB"
set NAIB.1 restype protein
set NAIB.1 name "NAIB"
# head = null
set NAIB tail NAIB.1.C
set NAIB.1 connect0 NAIB.1.N
set NAIB.1 connect1 NAIB.1.C
# set FF atom types for NAIB
set NAIB.1.N type N3
set NAIB.1.H1 type H
set NAIB.1.H2 type H
set NAIB.1.H3 type H
set NAIB.1.CA type CT
set NAIB.1.CB1 type CT
set NAIB.1.HB11 type HC
set NAIB.1.HB12 type HC
set NAIB.1.HB13 type HC
set NAIB.1.CB2 type CT
set NAIB.1.HB21 type HC
set NAIB.1.HB22 type HC
set NAIB.1.HB23 type HC
set NAIB.1.C type C
set NAIB.1.O type O
# save the OFF library for NAIB
saveoff NAIB NAIB.off

# set general information for CAIB
set CAIB name "CAIB"
set CAIB.1 restype protein
set CAIB.1 name "CAIB"
set CAIB head CAIB.1.N
# tail = null
set CAIB.1 connect0 CAIB.1.N
set CAIB.1 connect1 CAIB.1.C
# set FF atom types for CAIB
set CAIB.1.N type N
set CAIB.1.H type H
set CAIB.1.CA type CT
set CAIB.1.CB1 type CT
set CAIB.1.HB11 type HC
set CAIB.1.HB12 type HC
set CAIB.1.HB13 type HC
set CAIB.1.CB2 type CT
set CAIB.1.HB21 type HC
set CAIB.1.HB22 type HC
set CAIB.1.HB23 type HC
set CAIB.1.C type C
set CAIB.1.O type O2
set CAIB.1.OXT type O2
# save the OFF library for CAIB
saveoff CAIB CAIB.off

# Using the NAIB, AIB and CAIB libraries in LEaP
EXAMPLE = sequence { NAIB AIB CAIB }
# Optional ... Just to get an extended conformation
impose EXAMPLE {1 2 3}{{N CA C N 180.0}{C N CA C 180.0}{CA C N CA 180.0}{CA C N CA 180.0}{N CA C OXT 180.0}{C CA N H1 180.0}}

# quit