# R.E.DD.B. project F-59 # # Authors of the project: # F.-Y. Dupradeau, D. A. Case, C. Yu, R. Jimenez & F. E. Romesberg # # Please rename each tripos file: # tripos1.mol2 => HBA.mol2 # tripos2.mol2 => HBI.mol2 logFile leap-mol2tooff.log alias e edit alias q quit alias c charge verbosity 2 HBA = loadmol2 HBA.mol2 set HBA name "HBA" set HBA head HBA.1.P set HBA tail HBA.1.O3' set HBA.1 connect0 HBA.1.P set HBA.1 connect1 HBA.1.O3' set HBA.1 restype nucleic set HBA.1 name "HBA" # set FF atom types set HBA.1.P type P set HBA.1.O1P type O2 set HBA.1.O2P type O2 set HBA.1.O5' type OS set HBA.1.O3' type OS set HBA.1.C5' type CT set HBA.1.H5'1 type H1 set HBA.1.H5'2 type H1 set HBA.1.O4' type OS set HBA.1.C4' type CT set HBA.1.H4' type H1 set HBA.1.C3' type CT set HBA.1.H3' type H1 set HBA.1.C2' type CT set HBA.1.H2'1 type HC set HBA.1.H2'2 type HC set HBA.1.C1' type CT set HBA.1.H1' type H1 set HBA.1.N1 type NB set HBA.1.C1 type CK set HBA.1.O1 type OS set HBA.1.C2B type CB set HBA.1.C1B type CB set HBA.1.C3B type CA set HBA.1.H3B type HA set HBA.1.C4B type CA set HBA.1.H4B type HA set HBA.1.C5B type CA set HBA.1.H5B type HA set HBA.1.C6B type CA set HBA.1.H6B type HA set HBA.1.C3A type CA set HBA.1.H3A type HA set HBA.1.C4A type CA set HBA.1.H4A type HA set HBA.1.C5A type CA set HBA.1.C6A type CA set HBA.1.H6A type HA set HBA.1.C1A type CA set HBA.1.C2A type C set HBA.1.O2A type OH set HBA.1.H2A type HO # save the OFF library saveoff HBA HBA.off HBI = loadmol2 HBI.mol2 set HBI name "HBI" set HBI head HBI.1.P set HBI tail HBI.1.O3' set HBI.1 connect0 HBI.1.P set HBI.1 connect1 HBI.1.O3' set HBI.1 restype nucleic set HBI.1 name "HBI" # set FF atom types set HBI.1.P type P set HBI.1.O1P type O2 set HBI.1.O2P type O2 set HBI.1.O5' type OS set HBI.1.O3' type OS set HBI.1.C5' type CT set HBI.1.H5'1 type H1 set HBI.1.H5'2 type H1 set HBI.1.O4' type OS set HBI.1.C4' type CT set HBI.1.H4' type H1 set HBI.1.C3' type CT set HBI.1.H3' type H1 set HBI.1.C2' type CT set HBI.1.H2'1 type HC set HBI.1.H2'2 type HC set HBI.1.C1' type CT set HBI.1.H1' type H1 set HBI.1.N1 type NB set HBI.1.C1 type CK set HBI.1.O1 type OS set HBI.1.C2B type CB set HBI.1.C1B type CB set HBI.1.C3B type CA set HBI.1.H3B type HA set HBI.1.C4B type CA set HBI.1.H4B type HA set HBI.1.C5B type CA set HBI.1.H5B type HA set HBI.1.C6B type CA set HBI.1.H6B type HA set HBI.1.C3A type CA set HBI.1.C4A type CA set HBI.1.H4A type HA set HBI.1.C5A type CA set HBI.1.H5A type HA set HBI.1.C6A type CA set HBI.1.H6A type HA set HBI.1.C1A type CA set HBI.1.C2A type C set HBI.1.O2A type OH set HBI.1.H2A type HO # save the OFF library saveoff HBI HBI.off q