# R.E.DD.B. project F-51
#
# Authors of the project: 
# F.-Y. Dupradeau, A. Pigache, T. Zaffran, R. Lelong, N. Grivel & P. Cieplak
#
# January 2006

# Please rename each tripos file:
# tripos1.mol2 => RA3.mol2
# tripos2.mol2 => RA5.mol2
# tripos3.mol2 => RA.mol2
# tripos4.mol2 => RAN.mol2
# etc...

logFile leap-mol2tooff.log

alias e edit
alias q quit
alias c charge

verbosity 2

RA3 = loadmol2 RA3.mol2
set RA3 name "RA3"
set RA3 head RA3.1.P
# tail = null
set RA3.1 connect0 RA3.1.P
set RA3.1 connect1 RA3.1.H3T
set RA3.1 restype nucleic
set RA3.1 name "RA3"
# set FF atom types
set RA3.1.P type P
set RA3.1.O1P type O2
set RA3.1.O2P type O2
set RA3.1.O5' type OS
set RA3.1.O3' type OH
set RA3.1.H3T type HO
set RA3.1.C5' type CT
set RA3.1.H5'1 type H1
set RA3.1.H5'2 type H1
set RA3.1.O4' type OS
set RA3.1.C4' type CT
set RA3.1.H4' type H1
set RA3.1.C3' type CT
set RA3.1.H3' type H1
set RA3.1.C2' type CT
set RA3.1.H2'1 type H1
set RA3.1.O2' type OH
set RA3.1.HO'2 type HO
set RA3.1.C1' type CT
set RA3.1.H1' type H2
set RA3.1.N6 type N2
set RA3.1.H61 type H
set RA3.1.H62 type H
set RA3.1.C6 type CA
set RA3.1.C5 type CB
set RA3.1.N7 type NB
set RA3.1.C8 type CK
set RA3.1.H8 type H5
set RA3.1.N9 type "N*"
set RA3.1.C4 type CB
set RA3.1.N3 type NC
set RA3.1.C2 type CQ
set RA3.1.H2 type H5
set RA3.1.N1 type NC
# save the OFF library
saveoff RA3 RA3.off

RA5 = loadmol2 RA5.mol2
set RA5 name "RA5"
# head = null
set RA5 tail RA5.1.O3'
set RA5.1 connect0 RA5.1.H5T
set RA5.1 connect1 RA5.1.O3'
set RA5.1 restype nucleic
set RA5.1 name "RA5"
# set FF atom types
set RA5.1.O5' type OH
set RA5.1.H5T type HO
set RA5.1.O3' type OS
set RA5.1.C5' type CT
set RA5.1.H5'1 type H1
set RA5.1.H5'2 type H1
set RA5.1.O4' type OS
set RA5.1.C4' type CT
set RA5.1.H4' type H1
set RA5.1.C3' type CT
set RA5.1.H3' type H1
set RA5.1.C2' type CT
set RA5.1.H2'1 type H1
set RA5.1.O2' type OH
set RA5.1.HO'2 type HO
set RA5.1.C1' type CT
set RA5.1.H1' type H2
set RA5.1.N6 type N2
set RA5.1.H61 type H
set RA5.1.H62 type H
set RA5.1.C6 type CA
set RA5.1.C5 type CB
set RA5.1.N7 type NB
set RA5.1.C8 type CK
set RA5.1.H8 type H5
set RA5.1.N9 type "N*"
set RA5.1.C4 type CB
set RA5.1.N3 type NC
set RA5.1.C2 type CQ
set RA5.1.H2 type H5
set RA5.1.N1 type NC
# save the OFF library
saveoff RA5 RA5.off

RA = loadmol2 RA.mol2
set RA name "RA"
set RA head RA.1.P
set RA tail RA.1.O3'
set RA.1 connect0 RA.1.P
set RA.1 connect1 RA.1.O3'
set RA.1 restype nucleic
set RA.1 name "RA"
# set FF atom types
set RA.1.P type P
set RA.1.O1P type O2
set RA.1.O2P type O2
set RA.1.O5' type OS
set RA.1.O3' type OS
set RA.1.C5' type CT
set RA.1.H5'1 type H1
set RA.1.H5'2 type H1
set RA.1.O4' type OS
set RA.1.C4' type CT
set RA.1.H4' type H1
set RA.1.C3' type CT
set RA.1.H3' type H1
set RA.1.C2' type CT
set RA.1.H2'1 type H1
set RA.1.O2' type OH
set RA.1.HO'2 type HO
set RA.1.C1' type CT
set RA.1.H1' type H2
set RA.1.N6 type N2
set RA.1.H61 type H
set RA.1.H62 type H
set RA.1.C6 type CA
set RA.1.C5 type CB
set RA.1.N7 type NB
set RA.1.C8 type CK
set RA.1.H8 type H5
set RA.1.N9 type "N*"
set RA.1.C4 type CB
set RA.1.N3 type NC
set RA.1.C2 type CQ
set RA.1.H2 type H5
set RA.1.N1 type NC
# save the OFF library
saveoff RA RA.off

RAN = loadmol2 RAN.mol2
set RAN name "RAN"
# head & tail = null
set RAN.1 connect0 RAN.1.H5T
set RAN.1 connect1 RAN.1.H3T
set RAN.1 restype nucleic
set RAN.1 name "RAN"
# set FF atom types
set RAN.1.O5' type OH
set RAN.1.H5T type HO
set RAN.1.O3' type OH
set RAN.1.H3T type HO
set RAN.1.C5' type CT
set RAN.1.H5'1 type H1
set RAN.1.H5'2 type H1
set RAN.1.O4' type OS
set RAN.1.C4' type CT
set RAN.1.H4' type H1
set RAN.1.C3' type CT
set RAN.1.H3' type H1
set RAN.1.C2' type CT
set RAN.1.H2'1 type H1
set RAN.1.O2' type OH
set RAN.1.HO'2 type HO
set RAN.1.C1' type CT
set RAN.1.H1' type H2
set RAN.1.N6 type N2
set RAN.1.H61 type H
set RAN.1.H62 type H
set RAN.1.C6 type CA
set RAN.1.C5 type CB
set RAN.1.N7 type NB
set RAN.1.C8 type CK
set RAN.1.H8 type H5
set RAN.1.N9 type "N*"
set RAN.1.C4 type CB
set RAN.1.N3 type NC
set RAN.1.C2 type CQ
set RAN.1.H2 type H5
set RAN.1.N1 type NC
# save the OFF library
saveoff RAN RAN.off

# -------------------------

RC3 = loadmol2 RC3.mol2
set RC3 name "RC3"
set RC3 head RC3.1.P
# tail = null
set RC3.1 connect0 RC3.1.P
set RC3.1 connect1 RC3.1.H3T
set RC3.1 restype nucleic
set RC3.1 name "RC3"
# set FF atom types
set RC3.1.P type P
set RC3.1.O1P type O2
set RC3.1.O2P type O2
set RC3.1.O5' type OS
set RC3.1.O3' type OH
set RC3.1.H3T type HO
set RC3.1.C5' type CT
set RC3.1.H5'1 type H1
set RC3.1.H5'2 type H1
set RC3.1.O4' type OS
set RC3.1.C4' type CT
set RC3.1.H4' type H1
set RC3.1.C3' type CT
set RC3.1.H3' type H1
set RC3.1.C2' type CT
set RC3.1.H2'1 type H1
set RC3.1.O2' type OH
set RC3.1.HO'2 type HO
set RC3.1.C1' type CT
set RC3.1.H1' type H2
set RC3.1.N4 type N2
set RC3.1.H41 type H
set RC3.1.H42 type H
set RC3.1.C4 type CA
set RC3.1.N3 type NC
set RC3.1.C2 type C
set RC3.1.O2 type O
set RC3.1.N1 type "N*"
set RC3.1.C6 type CM
set RC3.1.H6 type H4
set RC3.1.C5 type CM
set RC3.1.H5 type HA
# save the OFF library
saveoff RC3 RC3.off

RC5 = loadmol2 RC5.mol2
set RC5 name "RC5"
# head = null
set RC5 tail RC5.1.O3'
set RC5.1 connect0 RC5.1.H5T
set RC5.1 connect1 RC5.1.O3'
set RC5.1 restype nucleic
set RC5.1 name "RC5"
# set FF atom types
set RC5.1.O5' type OH
set RC5.1.H5T type HO
set RC5.1.O3' type OS
set RC5.1.C5' type CT
set RC5.1.H5'1 type H1
set RC5.1.H5'2 type H1
set RC5.1.O4' type OS
set RC5.1.C4' type CT
set RC5.1.H4' type H1
set RC5.1.C3' type CT
set RC5.1.H3' type H1
set RC5.1.C2' type CT
set RC5.1.H2'1 type H1
set RC5.1.O2' type OH
set RC5.1.HO'2 type HO
set RC5.1.C1' type CT
set RC5.1.H1' type H2
set RC5.1.N4 type N2
set RC5.1.H41 type H
set RC5.1.H42 type H
set RC5.1.C4 type CA
set RC5.1.N3 type NC
set RC5.1.C2 type C
set RC5.1.O2 type O
set RC5.1.N1 type "N*"
set RC5.1.C6 type CM
set RC5.1.H6 type H4
set RC5.1.C5 type CM
set RC5.1.H5 type HA
# save the OFF library
saveoff RC5 RC5.off

RC = loadmol2 RC.mol2
set RC name "RC"
set RC head RC.1.P
set RC tail RC.1.O3'
set RC.1 connect0 RC.1.P
set RC.1 connect1 RC.1.O3'
set RC.1 restype nucleic
set RC.1 name "RC"
# set FF atom types
set RC.1.P type P
set RC.1.O1P type O2
set RC.1.O2P type O2
set RC.1.O5' type OS
set RC.1.O3' type OS
set RC.1.C5' type CT
set RC.1.H5'1 type H1
set RC.1.H5'2 type H1
set RC.1.O4' type OS
set RC.1.C4' type CT
set RC.1.H4' type H1
set RC.1.C3' type CT
set RC.1.H3' type H1
set RC.1.C2' type CT
set RC.1.H2'1 type H1
set RC.1.O2' type OH
set RC.1.HO'2 type HO
set RC.1.C1' type CT
set RC.1.H1' type H2
set RC.1.N4 type N2
set RC.1.H41 type H
set RC.1.H42 type H
set RC.1.C4 type CA
set RC.1.N3 type NC
set RC.1.C2 type C
set RC.1.O2 type O
set RC.1.N1 type "N*"
set RC.1.C6 type CM
set RC.1.H6 type H4
set RC.1.C5 type CM
set RC.1.H5 type HA
# save the OFF library
saveoff RC RC.off

RCN = loadmol2 RCN.mol2
set RCN name "RCN"
# head & tail = null
set RCN.1 connect0 RCN.1.H5T
set RCN.1 connect1 RCN.1.H3T
set RCN.1 restype nucleic
set RCN.1 name "RCN"
# set FF atom types
set RCN.1.O5' type OH
set RCN.1.H5T type HO
set RCN.1.O3' type OH
set RCN.1.H3T type HO
set RCN.1.C5' type CT
set RCN.1.H5'1 type H1
set RCN.1.H5'2 type H1
set RCN.1.O4' type OS
set RCN.1.C4' type CT
set RCN.1.H4' type H1
set RCN.1.C3' type CT
set RCN.1.H3' type H1
set RCN.1.C2' type CT
set RCN.1.H2'1 type H1
set RCN.1.O2' type OH
set RCN.1.HO'2 type HO
set RCN.1.C1' type CT
set RCN.1.H1' type H2
set RCN.1.N4 type N2
set RCN.1.H41 type H
set RCN.1.H42 type H
set RCN.1.C4 type CA
set RCN.1.N3 type NC
set RCN.1.C2 type C
set RCN.1.O2 type O
set RCN.1.N1 type "N*"
set RCN.1.C6 type CM
set RCN.1.H6 type H4
set RCN.1.C5 type CM
set RCN.1.H5 type HA
# save the OFF library
saveoff RCN RCN.off

# -------------------------

RG3 = loadmol2 RG3.mol2
set RG3 name "RG3"
set RG3 head RG3.1.P
# tail = null
set RG3.1 connect0 RG3.1.P
set RG3.1 connect1 RG3.1.H3T
set RG3.1 restype nucleic
set RG3.1 name "RG3"
# set FF atom types
set RG3.1.P type P
set RG3.1.O1P type O2
set RG3.1.O2P type O2
set RG3.1.O5' type OS
set RG3.1.O3' type OH
set RG3.1.H3T type HO
set RG3.1.C5' type CT
set RG3.1.H5'1 type H1
set RG3.1.H5'2 type H1
set RG3.1.O4' type OS
set RG3.1.C4' type CT
set RG3.1.H4' type H1
set RG3.1.C3' type CT
set RG3.1.H3' type H1
set RG3.1.C2' type CT
set RG3.1.H2'1 type H1
set RG3.1.O2' type OH
set RG3.1.HO'2 type HO
set RG3.1.C1' type CT
set RG3.1.H1' type H2
set RG3.1.N2 type N2
set RG3.1.H21 type H
set RG3.1.H22 type H
set RG3.1.O6 type O
set RG3.1.C6 type C
set RG3.1.C5 type CB
set RG3.1.N7 type NB
set RG3.1.C8 type CK
set RG3.1.H8 type H5
set RG3.1.N9 type "N*"
set RG3.1.C4 type CB
set RG3.1.N3 type NC
set RG3.1.C2 type CA
set RG3.1.N1 type NA
set RG3.1.H1 type H
# save the OFF library
saveoff RG3 RG3.off

RG5 = loadmol2 RG5.mol2
set RG5 name "RG5"
# head = null
set RG5 tail RG5.1.O3'
set RG5.1 connect0 RG5.1.H5T
set RG5.1 connect1 RG5.1.O3'
set RG5.1 restype nucleic
set RG5.1 name "RG5"
# set FF atom types
set RG5.1.O5' type OH
set RG5.1.H5T type HO
set RG5.1.O3' type OS
set RG5.1.C5' type CT
set RG5.1.H5'1 type H1
set RG5.1.H5'2 type H1
set RG5.1.O4' type OS
set RG5.1.C4' type CT
set RG5.1.H4' type H1
set RG5.1.C3' type CT
set RG5.1.H3' type H1
set RG5.1.C2' type CT
set RG5.1.H2'1 type H1
set RG5.1.O2' type OH
set RG5.1.HO'2 type HO
set RG5.1.C1' type CT
set RG5.1.H1' type H2
set RG5.1.N2 type N2
set RG5.1.H21 type H
set RG5.1.H22 type H
set RG5.1.O6 type O
set RG5.1.C6 type C
set RG5.1.C5 type CB
set RG5.1.N7 type NB
set RG5.1.C8 type CK
set RG5.1.H8 type H5
set RG5.1.N9 type "N*"
set RG5.1.C4 type CB
set RG5.1.N3 type NC
set RG5.1.C2 type CA
set RG5.1.N1 type NA
set RG5.1.H1 type H
# save the OFF library
saveoff RG5 RG5.off

RG = loadmol2 RG.mol2
set RG name "RG"
set RG head RG.1.P
set RG tail RG.1.O3'
set RG.1 connect0 RG.1.P
set RG.1 connect1 RG.1.O3'
set RG.1 restype nucleic
set RG.1 name "RG"
# set FF atom types
set RG.1.P type P
set RG.1.O1P type O2
set RG.1.O2P type O2
set RG.1.O5' type OS
set RG.1.O3' type OS
set RG.1.C5' type CT
set RG.1.H5'1 type H1
set RG.1.H5'2 type H1
set RG.1.O4' type OS
set RG.1.C4' type CT
set RG.1.H4' type H1
set RG.1.C3' type CT
set RG.1.H3' type H1
set RG.1.C2' type CT
set RG.1.H2'1 type H1
set RG.1.O2' type OH
set RG.1.HO'2 type HO
set RG.1.C1' type CT
set RG.1.H1' type H2
set RG.1.N2 type N2
set RG.1.H21 type H
set RG.1.H22 type H
set RG.1.O6 type O
set RG.1.C6 type C
set RG.1.C5 type CB
set RG.1.N7 type NB
set RG.1.C8 type CK
set RG.1.H8 type H5
set RG.1.N9 type "N*"
set RG.1.C4 type CB
set RG.1.N3 type NC
set RG.1.C2 type CA
set RG.1.N1 type NA
set RG.1.H1 type H
# save the OFF library
saveoff RG RG.off

RGN = loadmol2 RGN.mol2
set RGN name "RGN"
# head & tail = null
set RGN.1 connect0 RGN.1.H5T
set RGN.1 connect1 RGN.1.H3T
set RGN.1 restype nucleic
set RGN.1 name "RGN"
# set FF atom types
set RGN.1.O5' type OH
set RGN.1.H5T type HO
set RGN.1.O3' type OH
set RGN.1.H3T type HO
set RGN.1.C5' type CT
set RGN.1.H5'1 type H1
set RGN.1.H5'2 type H1
set RGN.1.O4' type OS
set RGN.1.C4' type CT
set RGN.1.H4' type H1
set RGN.1.C3' type CT
set RGN.1.H3' type H1
set RGN.1.C2' type CT
set RGN.1.H2'1 type H1
set RGN.1.O2' type OH
set RGN.1.HO'2 type HO
set RGN.1.C1' type CT
set RGN.1.H1' type H2
set RGN.1.N2 type N2
set RGN.1.H21 type H
set RGN.1.H22 type H
set RGN.1.O6 type O
set RGN.1.C6 type C
set RGN.1.C5 type CB
set RGN.1.N7 type NB
set RGN.1.C8 type CK
set RGN.1.H8 type H5
set RGN.1.N9 type "N*"
set RGN.1.C4 type CB
set RGN.1.N3 type NC
set RGN.1.C2 type CA
set RGN.1.N1 type NA
set RGN.1.H1 type H
# save the OFF library
saveoff RGN RGN.off

# -------------------------

RU3 = loadmol2 RU3.mol2
set RU3 name "RU3"
set RU3 head RU3.1.P
# tail = null
set RU3.1 connect0 RU3.1.P
set RU3.1 connect1 RU3.1.H3T
set RU3.1 restype nucleic
set RU3.1 name "RU3"
# set FF atom types
set RU3.1.P type P
set RU3.1.O1P type O2
set RU3.1.O2P type O2
set RU3.1.O5' type OS
set RU3.1.O3' type OH
set RU3.1.H3T type HO
set RU3.1.C5' type CT
set RU3.1.H5'1 type H1
set RU3.1.H5'2 type H1
set RU3.1.O4' type OS
set RU3.1.C4' type CT
set RU3.1.H4' type H1
set RU3.1.C3' type CT
set RU3.1.H3' type H1
set RU3.1.C2' type CT
set RU3.1.H2'1 type H1
set RU3.1.O2' type OH
set RU3.1.HO'2 type HO
set RU3.1.C1' type CT
set RU3.1.H1' type H2
set RU3.1.O4 type O
set RU3.1.C4 type C
set RU3.1.N3 type NA
set RU3.1.H3 type H
set RU3.1.C2 type C
set RU3.1.O2 type O
set RU3.1.N1 type "N*"
set RU3.1.C6 type CM
set RU3.1.H6 type H4
set RU3.1.C5 type CM
set RU3.1.H5 type HA
# save the OFF library
saveoff RU3 RU3.off

RU5 = loadmol2 RU5.mol2
set RU5 name "RU5"
# head = null
set RU5 tail RU5.1.O3'
set RU5.1 connect0 RU5.1.H5T
set RU5.1 connect1 RU5.1.O3'
set RU5.1 restype nucleic
set RU5.1 name "RU5"
# set FF atom types
set RU5.1.O5' type OH
set RU5.1.H5T type HO
set RU5.1.O3' type OS
set RU5.1.C5' type CT
set RU5.1.H5'1 type H1
set RU5.1.H5'2 type H1
set RU5.1.O4' type OS
set RU5.1.C4' type CT
set RU5.1.H4' type H1
set RU5.1.C3' type CT
set RU5.1.H3' type H1
set RU5.1.C2' type CT
set RU5.1.H2'1 type H1
set RU5.1.O2' type OH
set RU5.1.HO'2 type HO
set RU5.1.C1' type CT
set RU5.1.H1' type H2
set RU5.1.O4 type O
set RU5.1.C4 type C
set RU5.1.N3 type NA
set RU5.1.H3 type H
set RU5.1.C2 type C
set RU5.1.O2 type O
set RU5.1.N1 type "N*"
set RU5.1.C6 type CM
set RU5.1.H6 type H4
set RU5.1.C5 type CM
set RU5.1.H5 type HA
# save the OFF library
saveoff RU5 RU5.off

RU = loadmol2 RU.mol2
set RU name "RU"
set RU head RU.1.P
set RU tail RU.1.O3'
set RU.1 connect0 RU.1.P
set RU.1 connect1 RU.1.O3'
set RU.1 restype nucleic
set RU.1 name "RU"
# set FF atom types
set RU.1.P type P
set RU.1.O1P type O2
set RU.1.O2P type O2
set RU.1.O5' type OS
set RU.1.O3' type OS
set RU.1.C5' type CT
set RU.1.H5'1 type H1
set RU.1.H5'2 type H1
set RU.1.O4' type OS
set RU.1.C4' type CT
set RU.1.H4' type H1
set RU.1.C3' type CT
set RU.1.H3' type H1
set RU.1.C2' type CT
set RU.1.H2'1 type H1
set RU.1.O2' type OH
set RU.1.HO'2 type HO
set RU.1.C1' type CT
set RU.1.H1' type H2
set RU.1.O4 type O
set RU.1.C4 type C
set RU.1.N3 type NA
set RU.1.H3 type H
set RU.1.C2 type C
set RU.1.O2 type O
set RU.1.N1 type "N*"
set RU.1.C6 type CM
set RU.1.H6 type H4
set RU.1.C5 type CM
set RU.1.H5 type HA
# save the OFF library
saveoff RU RU.off

RUN = loadmol2 RUN.mol2
set RUN name "RUN"
# head & tail = null
set RUN.1 connect0 RUN.1.H5T
set RUN.1 connect1 RUN.1.H3T
set RUN.1 restype nucleic
set RUN.1 name "RUN"
# set FF atom types
set RUN.1.O5' type OH
set RUN.1.H5T type HO
set RUN.1.O3' type OH
set RUN.1.H3T type HO
set RUN.1.C5' type CT
set RUN.1.H5'1 type H1
set RUN.1.H5'2 type H1
set RUN.1.O4' type OS
set RUN.1.C4' type CT
set RUN.1.H4' type H1
set RUN.1.C3' type CT
set RUN.1.H3' type H1
set RUN.1.C2' type CT
set RUN.1.H2'1 type H1
set RUN.1.O2' type OH
set RUN.1.HO'2 type HO
set RUN.1.C1' type CT
set RUN.1.H1' type H2
set RUN.1.O4 type O
set RUN.1.C4 type C
set RUN.1.N3 type NA
set RUN.1.H3 type H
set RUN.1.C2 type C
set RUN.1.O2 type O
set RUN.1.N1 type "N*"
set RUN.1.C6 type CM
set RUN.1.H6 type H4
set RUN.1.C5 type CM
set RUN.1.H5 type HA
# save the OFF library
saveoff RUN RUN.off

# q