# R.E.DD.B. project F-72 # # Authors of the projects: # F.-Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, D, Lelong, W. Rosanski, N. Grivel & P. Cieplak # # February 2009 # # Please rename each tripos file as they should be... # tripos$n.mol2 => TMM1.mol2 $n=1 single conformation (alpha helix) charge fit; dipeptide # tripos$n.mol2 => TMM2.mol2 $n=2 single conformation (beta sheet) charge fit; dipeptide # tripos$n.mol2 => TMM3.mol2 $n=3 two conformation (alpha helix + beta sheet) charge fit; dipeptide # choose TMM1.mol2, TMM2.mol2 or TMM3.mol2 in this script, but do NOT load the three versions in same time! # # tripos$n.mol2 => TYM1.mol2 $n=4 single conformation charge fit; central fragment # tripos$n.mol2 => TYM2.mol2 $n=5 single conformation charge fit; central fragment # tripos$n.mol2 => TYM3.mol2 $n=6 two conformation charge fit; central fragment # choose TYM1.mol2, TYM2.mol2 or TYM3.mol2 in this script, but do NOT load the three versions in same time! # # tripos$n.mol2 => NTYM1.mol2 $n=7 single conformation charge fit; N-terminal fragment # tripos$n.mol2 => NTYM2.mol2 $n=8 single conformation charge fit; N-terminal fragment # tripos$n.mol2 => NTYM3.mol2 $n=9 two conformation charge fit; N-terminal fragment # choose NTYM1.mol2, NNTYM2.mol2 or NTYM3.mol2 in this script, but do NOT load the three versions in same time! # # tripos$n.mol2 => CTYM1.mol2 $n=10 single conformation charge fit; C-terminal fragment # tripos$n.mol2 => CTYM2.mol2 $n=11 single conformation charge fit; C-terminal fragment # tripos$n.mol2 => CTYM3.mol2 $n=12 two conformation charge fit; C-terminal fragment # choose CTYM1.mol2, CTYM2.mol2 or CTYM3.mol2 in this script, but do NOT load the three versions in same time! logFile leap-mol2tooff.log alias e edit alias q quit alias c charge verbosity 2 source leaprc.ff99SB ### dipeptide # TMM = loadmol2 TMM1.mol2 # TMM = loadmol2 TMM2.mol2 # TMM = loadmol2 TMM3.mol2 TMM = loadmol2 mm3-o2.mol2 set TMM name "TMM" set TMM.1 name "ACE" set TMM.2 name "TYM" set TMM.3 name "NME" set TMM.1 restype protein set TMM.2 restype protein set TMM.3 restype protein # set FF atom types set TMM.1.C1 type CT set TMM.1.H11 type HC set TMM.1.H12 type HC set TMM.1.H13 type HC set TMM.1.C type C set TMM.1.O type O set TMM.2.N type N set TMM.2.H type H set TMM.2.C type C set TMM.2.O type O set TMM.2.CA type CT set TMM.2.HA type H1 set TMM.2.CB type CT set TMM.2.HB1 type HC set TMM.2.HB2 type HC set TMM.2.CG type CA set TMM.2.CD1 type CA set TMM.2.HD1 type HA set TMM.2.CD2 type CA set TMM.2.HD2 type HA set TMM.2.CE1 type CA set TMM.2.HE1 type HA set TMM.2.CE2 type CA set TMM.2.HE2 type HA set TMM.2.CZ type C set TMM.2.OZ type OS set TMM.2.CM type CT set TMM.2.HM1 type H1 set TMM.2.HM2 type H1 set TMM.2.HM3 type H1 set TMM.3.N type N set TMM.3.H type H set TMM.3.C2 type CT set TMM.3.H21 type H1 set TMM.3.H22 type H1 set TMM.3.H23 type H1 ### Central Fragment # TYM = loadmol2 TYM1.mol2 # TYM = loadmol2 TYM2.mol2 # TYM = loadmol2 TYM3.mol2 TYM = loadmol2 mm6-o2.FG2.mol2 set TYM name "TYM" set TYM head TYM.1.N set TYM tail TYM.1.C set TYM.1 connect0 TYM.1.N set TYM.1 connect1 TYM.1.C set TYM.1 restype protein set TYM.1 name "TYM" # set FF atom types set TYM.1.N type N set TYM.1.H type H set TYM.1.C type C set TYM.1.O type O set TYM.1.CA type CT set TYM.1.HA type H1 set TYM.1.CB type CT set TYM.1.HB1 type HC set TYM.1.HB2 type HC set TYM.1.CG type CA set TYM.1.CD1 type CA set TYM.1.HD1 type HA set TYM.1.CD2 type CA set TYM.1.HD2 type HA set TYM.1.CE1 type CA set TYM.1.HE1 type HA set TYM.1.CE2 type CA set TYM.1.HE2 type HA set TYM.1.CZ type C set TYM.1.OZ type OS set TYM.1.CM type CT set TYM.1.HM1 type H1 set TYM.1.HM2 type H1 set TYM.1.HM3 type H1 ### N-terminal Fragment # NTYM = loadmol2 NTYM1.mol2 # NTYM = loadmol2 NTYM2.mol2 # NTYM = loadmol2 NTYM3.mol2 NTYM = loadmol2 mm12-o2-FG.mol2 set NTYM name "NTYM" # head = null set NTYM tail NTYM.1.C set NTYM.1 connect0 NTYM.1.N set NTYM.1 connect1 NTYM.1.C set NTYM.1 restype protein set NTYM.1 name "NTYM" # set FF atom types set NTYM.1.N type N3 set NTYM.1.H1 type H set NTYM.1.H2 type H set NTYM.1.H3 type H set NTYM.1.CA type CT set NTYM.1.HA type HP set NTYM.1.C type C set NTYM.1.O type O set NTYM.1.CB type CT set NTYM.1.HB1 type HC set NTYM.1.HB2 type HC set NTYM.1.CG type CA set NTYM.1.CD1 type CA set NTYM.1.HD1 type HA set NTYM.1.CD2 type CA set NTYM.1.HD2 type HA set NTYM.1.CE1 type CA set NTYM.1.HE1 type HA set NTYM.1.CE2 type CA set NTYM.1.HE2 type HA set NTYM.1.CZ type C set NTYM.1.OZ type OS set NTYM.1.CM type CT set NTYM.1.HM1 type H1 set NTYM.1.HM2 type H1 set NTYM.1.HM3 type H1 # CTYM = loadmol2 CTYM1.mol2 # CTYM = loadmol2 CTYM2.mol2 # CTYM = loadmol2 CTYM3.mol2 CTYM = loadmol2 mm18-o2-FG.mol2 set CTYM name "CTYM" set CTYM head CTYM.1.N # tail = null set CTYM.1 connect0 CTYM.1.N set CTYM.1 connect1 CTYM.1.C set CTYM.1 restype protein set CTYM.1 name "CTYM" # set FF atom types set CTYM.1.N type N set CTYM.1.H type H set CTYM.1.CA type CT set CTYM.1.HA type H1 set CTYM.1.CB type CT set CTYM.1.HB1 type HC set CTYM.1.HB2 type HC set CTYM.1.CG type CA set CTYM.1.CD1 type CA set CTYM.1.HD1 type HA set CTYM.1.CD2 type CA set CTYM.1.HD2 type HA set CTYM.1.CE1 type CA set CTYM.1.HE1 type HA set CTYM.1.CE2 type CA set CTYM.1.HE2 type HA set CTYM.1.CZ type C set CTYM.1.OZ type OS set CTYM.1.CM type CT set CTYM.1.HM1 type H1 set CTYM.1.HM2 type H1 set CTYM.1.HM3 type H1 set CTYM.1.C type C set CTYM.1.O type O2 set CTYM.1.OXT type O2 # save the OFF library saveoff TMM q4md-forcefieldtools.off saveoff TYM q4md-forcefieldtools.off saveoff NTYM q4md-forcefieldtools.off saveoff CTYM q4md-forcefieldtools.off # Just to test TEST = sequence { NTYM TYM CTYM }