# R.E.DD.B. projects W-46, W-47, W-48 & W-49 # # Authors of the project: # F.-Y. Dupradeau, A. Pigache, T. Zaffran, R. Lelong, N. Grivel and P. Cieplak # # tripos1.mol2 => Dimethylsulfoxide # tripos2.mol2 => Ethanol # tripos3.mol2 => Trifluoroethanol # tripos4.mol2 => methanol # tripos5.mol2 => Acetone # tripos6.mol2 => Acetic acid # tripos7.mol2 => Acetonitrile # tripos8.mol2 => Benzene # tripos9.mol2 => Toluene # tripos10.mol2 => Chloroforme # etc... logFile leap-mol2tooff.log alias e edit alias q quit alias c charge verbosity 2 source leaprc.ff99 # FRCMOD = loadamberparams YOUR-FRCMOD-FILE addAtomTypes { # { "CX" "C" "sp" } # { "NX" "N" "sp" } { "OX" "O" "sp2" } { "SX" "S" "sp3" } } DMSO = loadmol2 tripos1.mol2 ETOH = loadmol2 tripos2.mol2 TFE = loadmol2 tripos3.mol2 MEOH = loadmol2 tripos4.mol2 ACT = loadmol2 tripos5.mol2 ACOH = loadmol2 tripos6.mol2 ACN = loadmol2 tripos7.mol2 BNZ = loadmol2 tripos8.mol2 TOL = loadmol2 tripos9.mol2 CHL = loadmol2 tripos10.mol2 # tripos1.mol2 set DMSO name "DMSO" # head & tail not needed since whole molecule # connect0 & connect1 not needed since whole molecule set DMSO.1 restype solvent set DMSO.1 name "DMSO" # set FF atom types set DMSO.1.C1 type CT set DMSO.1.H11 type H1 set DMSO.1.H12 type H1 set DMSO.1.H13 type H1 # You might prefer to add your own FF atom types for S2 & O3 set DMSO.1.S2 type SX set DMSO.1.O3 type OX set DMSO.1.C4 type CT set DMSO.1.H41 type H1 set DMSO.1.H42 type H1 set DMSO.1.H43 type H1 # save the OFF library saveoff DMSO DMSO.off # tripos2.mol2 set ETOH name "ETOH" # head & tail not needed since whole molecule # connect0 & connect1 not needed since whole molecule set ETOH.1 restype solvent set ETOH.1 name "ETOH" # set FF atom types set ETOH.1.C1 type CT set ETOH.1.H11 type HC set ETOH.1.H12 type HC set ETOH.1.H13 type HC set ETOH.1.C2 type CT set ETOH.1.H21 type H1 set ETOH.1.H22 type H1 set ETOH.1.O3 type OH set ETOH.1.H3 type HO # save the OFF library saveoff ETOH ETOH.off # tripos3.mol2 set TFE name "TFE" # head & tail not needed since whole molecule # connect0 & connect1 not needed since whole molecule set TFE.1 restype solvent set TFE.1 name "TFE" # set FF atom types set TFE.1.C1 type CT set TFE.1.F11 type F set TFE.1.F12 type F set TFE.1.F13 type F set TFE.1.C2 type CT set TFE.1.H21 type H1 set TFE.1.H22 type H1 set TFE.1.O3 type OH set TFE.1.H3 type HO # save the OFF library saveoff TFE TFE.off # tripos4.mol2 set MEOH name "MEOH" # head & tail not needed since whole molecule # connect0 & connect1 not needed since whole molecule set MEOH.1 restype solvent set MEOH.1 name "MEOH" # set FF atom types set MEOH.1.C1 type CT set MEOH.1.H11 type H1 set MEOH.1.H12 type H1 set MEOH.1.H13 type H1 set MEOH.1.O2 type OH set MEOH.1.H2 type HO # save the OFF library saveoff MEOH MEOH.off # tripos5.mol2 set ACT name "ACT" # head & tail not needed since whole molecule # connect0 & connect1 not needed since whole molecule set ACT.1 restype solvent set ACT.1 name "ACT" # set FF atom types set ACT.1.C1 type CT set ACT.1.H11 type HC set ACT.1.H12 type HC set ACT.1.H13 type HC set ACT.1.C2 type C set ACT.1.O3 type O set ACT.1.C4 type CT set ACT.1.H41 type HC set ACT.1.H42 type HC set ACT.1.H43 type HC # save the OFF library saveoff ACT ACT.off # tripos6.mol2 set ACOH name "ACOH" # head & tail not needed since whole molecule # connect0 & connect1 not needed since whole molecule set ACOH.1 restype solvent set ACOH.1 name "ACOH" # set FF atom types set ACOH.1.C1 type CT set ACOH.1.H11 type HC set ACOH.1.H12 type HC set ACOH.1.H13 type HC set ACOH.1.C2 type C set ACOH.1.O3 type O set ACOH.1.O4 type OH set ACOH.1.H5 type HO # save the OFF library saveoff ACOH ACOH.off # tripos7.mol2 set ACN name "ACN" # head & tail not needed since whole molecule # connect0 & connect1 not needed since whole molecule set ACN.1 restype solvent set ACN.1 name "ACN" # set FF atom types set ACN.1.C1 type CT set ACN.1.H11 type HC set ACN.1.H12 type HC set ACN.1.H13 type HC # You might prefer to add your own FF atom types for C2 & N3 set ACN.1.C2 type CX set ACN.1.N3 type NX saveoff ACN ACN.off # tripos8.mol2 set BNZ name "BNZ" # head & tail not needed since whole molecule # connect0 & connect1 not needed since whole molecule set BNZ.1 restype solvent set BNZ.1 name "BNZ" # set FF atom types set BNZ.1.C1 type CA set BNZ.1.H1 type HA set BNZ.1.C2 type CA set BNZ.1.H2 type HA set BNZ.1.C3 type CA set BNZ.1.H3 type HA set BNZ.1.C4 type CA set BNZ.1.H4 type HA set BNZ.1.C5 type CA set BNZ.1.H5 type HA set BNZ.1.C6 type CA set BNZ.1.H6 type HA # save the OFF library saveoff BNZ BNZ.off # tripos9.mol2 set TOL name "TOL" # head & tail not needed since whole molecule # connect0 & connect1 not needed since whole molecule set TOL.1 restype solvent set TOL.1 name "TOL" # set FF atom types set TOL.1.C1 type CT set TOL.1.H11 type HC set TOL.1.H12 type HC set TOL.1.H13 type HC set TOL.1.C2 type CA set TOL.1.C3 type CA set TOL.1.H3 type HA set TOL.1.C4 type CA set TOL.1.H4 type HA set TOL.1.C5 type CA set TOL.1.H5 type HA set TOL.1.C6 type CA set TOL.1.H6 type HA set TOL.1.C7 type CA set TOL.1.H7 type HA # save the OFF library saveoff TOL TOL.off # tripos10.mol2 set CHL name "CHL" # head & tail not needed since whole molecule # connect0 & connect1 not needed since whole molecule set CHL.1 restype solvent set CHL.1 name "CHL" # set FF atom types set CHL.1.C1 type CT set CHL.1.H2 type H3 set CHL.1.CL3 type CL set CHL.1.CL4 type CL set CHL.1.CL5 type CL # save the OFF library saveoff CHL CHL.off # q