# R.E.DD.B. projects F-1, F-2, F-3, F-7, F-11, F-15 & F-19 # # Authors of the projects: # F.-Y. Dupradeau, A. Pigache, T. Zaffran, R. Lelong, N. Grivel & P. Cieplak # # January 2006 # # Please rename each tripos file as they should... # tripos$n.mol2 => AIB.mol2 $n=1 R.E.DD.B. projects F-1, F-2 or F-3 # tripos$n.mol2 => NAIB.mol2 $n=1 R.E.DD.B. project F-7 # tripos$n.mol2 => CAIB.mol2 $n=1 R.E.DD.B. project F-11 # tripos$n.mol2 => N0AI.mol2 $n=1 R.E.DD.B. project F-15 # tripos$n.mol2 => C0AI.mol2 $n=1 R.E.DD.B. project F-19 logFile leap-mol2tooff.log alias e edit alias q quit alias c charge verbosity 2 AIB = loadmol2 AIB.mol2 set AIB 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 AIB.1 restype protein set AIB.1 name "AIB" # set FF atom types set AIB.1.N type N set AIB.1.H type H set AIB.1.C type C set AIB.1.O type O 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 # save the OFF library saveoff AIB AIB.off NAIB = loadmol2 NAIB.mol2 set NAIB 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 NAIB.1 restype protein set NAIB.1 name "NAIB" # set FF atom types 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.C type C set NAIB.1.O type O 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 # save the OFF library saveoff NAIB NAIB.off CAIB = loadmol2 CAIB.mol2 set CAIB 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 CAIB.1 restype protein set CAIB.1 name "CAIB" # set FF atom types set CAIB.1.N type N set CAIB.1.H type H set CAIB.1.C type C set CAIB.1.O type O2 set CAIB.1.OXT type O2 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 # save the OFF library saveoff CAIB CAIB.off N0AI = loadmol2 N0AI.mol2 set N0AI name "N0AI" # head = null set N0AI tail N0AI.1.C set N0AI.1 connect0 N0AI.1.N set N0AI.1 connect1 N0AI.1.C set N0AI.1 restype protein set N0AI.1 name "N0AI" # set FF atom types set N0AI.1.N type N3 set N0AI.1.H1 type H set N0AI.1.H2 type H set N0AI.1.C type C set N0AI.1.O type O set N0AI.1.CA type CT set N0AI.1.CB1 type CT set N0AI.1.HB11 type HC set N0AI.1.HB12 type HC set N0AI.1.HB13 type HC set N0AI.1.CB2 type CT set N0AI.1.HB21 type HC set N0AI.1.HB22 type HC set N0AI.1.HB23 type HC # save the OFF library saveoff N0AI N0AI.off C0AI = loadmol2 C0AI.mol2 set C0AI name "C0AI" set C0AI head C0AI.1.N # tail = null set C0AI.1 connect0 C0AI.1.N set C0AI.1 connect1 C0AI.1.C set C0AI.1 restype protein set C0AI.1 name "C0AI" # set FF atom types set C0AI.1.N type N set C0AI.1.H type H set C0AI.1.C type C set C0AI.1.O type O2 set C0AI.1.OXT type OH set C0AI.1.HXT type HO set C0AI.1.CA type CT set C0AI.1.CB1 type CT set C0AI.1.HB11 type HC set C0AI.1.HB12 type HC set C0AI.1.HB13 type HC set C0AI.1.CB2 type CT set C0AI.1.HB21 type HC set C0AI.1.HB22 type HC set C0AI.1.HB23 type HC # save the OFF library saveoff C0AI C0AI.off # quit