# R.E.DD.B. project F-57 # # Authors of the project: # F.-Y. Dupradeau, D. A. Case, C. Yu, R. Jimenez & F. E. Romesberg # # Please rename each tripos file: # tripos1.mol2 => ABA3.mol2 # tripos2.mol2 => ABA5.mol2 # tripos3.mol2 => ABA.mol2 # tripos4.mol2 => ABAN.mol2 # etc... logFile leap-mol2tooff.log alias e edit alias q quit alias c charge verbosity 2 ABA3 = loadmol2 ABA3.mol2 set ABA3 name "ABA3" set ABA3 head ABA3.1.P # tail = null set ABA3.1 connect0 ABA3.1.P set ABA3.1 connect1 ABA3.1.H3T set ABA3.1 restype nucleic set ABA3.1 name "ABA3" # set FF atom types set ABA3.1.P type P set ABA3.1.O1P type O2 set ABA3.1.O2P type O2 set ABA3.1.O5' type OS set ABA3.1.O3' type OH set ABA3.1.H3T type HO set ABA3.1.C5' type CT set ABA3.1.H5'1 type H1 set ABA3.1.H5'2 type H1 set ABA3.1.O4' type OS set ABA3.1.C4' type CT set ABA3.1.H4' type H1 set ABA3.1.C3' type CT set ABA3.1.H3' type H1 set ABA3.1.C2' type CT set ABA3.1.H2'1 type HC set ABA3.1.H2'2 type HC set ABA3.1.C1' type CT set ABA3.1.H1'1 type H1 set ABA3.1.H1'2 type H1 # save the OFF library saveoff ABA3 ABA3.off ABA5 = loadmol2 ABA5.mol2 set ABA5 name "ABA5" # head = null set ABA5 tail ABA5.1.O3' set ABA5.1 connect0 ABA5.1.H5T set ABA5.1 connect1 ABA5.1.O3' set ABA5.1 restype nucleic set ABA5.1 name "ABA5" # set FF atom types set ABA5.1.O5' type OH set ABA5.1.H5T type HO set ABA5.1.O3' type OS set ABA5.1.C5' type CT set ABA5.1.H5'1 type H1 set ABA5.1.H5'2 type H1 set ABA5.1.O4' type OS set ABA5.1.C4' type CT set ABA5.1.H4' type H1 set ABA5.1.C3' type CT set ABA5.1.H3' type H1 set ABA5.1.C2' type CT set ABA5.1.H2'1 type HC set ABA5.1.H2'2 type HC set ABA5.1.C1' type CT set ABA5.1.H1'1 type H1 set ABA5.1.H1'2 type H1 # save the OFF library saveoff ABA5 ABA5.off ABA = loadmol2 ABA.mol2 set ABA name "ABA" set ABA head ABA.1.P set ABA tail ABA.1.O3' set ABA.1 connect0 ABA.1.P set ABA.1 connect1 ABA.1.O3' set ABA.1 restype nucleic set ABA.1 name "ABA" # set FF atom types set ABA.1.P type P set ABA.1.O1P type O2 set ABA.1.O2P type O2 set ABA.1.O5' type OS set ABA.1.O3' type OS set ABA.1.C5' type CT set ABA.1.H5'1 type H1 set ABA.1.H5'2 type H1 set ABA.1.O4' type OS set ABA.1.C4' type CT set ABA.1.H4' type H1 set ABA.1.C3' type CT set ABA.1.H3' type H1 set ABA.1.C2' type CT set ABA.1.H2'1 type HC set ABA.1.H2'2 type HC set ABA.1.C1' type CT set ABA.1.H1'1 type H1 set ABA.1.H1'2 type H1 # save the OFF library saveoff ABA ABA.off ABAN = loadmol2 ABAN.mol2 set ABAN name "ABAN" # head & tail = null set ABAN.1 connect0 ABAN.1.H5T set ABAN.1 connect1 ABAN.1.H3T set ABAN.1 restype nucleic set ABAN.1 name "ABAN" # set FF atom types set ABAN.1.O5' type OH set ABAN.1.H5T type HO set ABAN.1.O3' type OH set ABAN.1.H3T type HO set ABAN.1.C5' type CT set ABAN.1.H5'1 type H1 set ABAN.1.H5'2 type H1 set ABAN.1.O4' type OS set ABAN.1.C4' type CT set ABAN.1.H4' type H1 set ABAN.1.C3' type CT set ABAN.1.H3' type H1 set ABAN.1.C2' type CT set ABAN.1.H2'1 type HC set ABAN.1.H2'2 type HC set ABAN.1.C1' type CT set ABAN.1.H1'1 type H1 set ABAN.1.H1'2 type H1 # save the OFF library saveoff ABAN ABAN.off q