-I: Adding /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/prep to search path. -I: Adding /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib to search path. -I: Adding /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm to search path. -I: Adding /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/cmd to search path. -s: Ignoring startup file: leaprc -f: Source buildit-vac.in. Welcome to LEaP! Sourcing: ./buildit-vac.in Could not open file ./leaprc.ff99bsc0: No such file or directory Loading library: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/lib/RNA_CI.lib Could not open file frcmod.tip3p: not found Loading parameters: /oasis/projects/nsf/slc216/droe/GIT/amber/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) Could not open file frcmod.ff99Chen-Garcia: not found Checking 'm'.... WARNING: The unperturbed charge of the unit: -1.000000 is not zero. Warning: Close contact of 1.127838 angstroms between .R.A and .R.A Checking parameters for unit 'm'. Checking for bond parameters. Could not find bond parameter for: OS - P Could not find bond parameter for: OH - HO Could not find bond parameter for: CT - H1 Could not find bond parameter for: CT - OH Could not find bond parameter for: CT - H1 Could not find bond parameter for: CT - CT Could not find bond parameter for: CT - OS Could not find bond parameter for: NC - CB Could not find bond parameter for: CQ - H5 Could not find bond parameter for: CQ - NC Could not find bond parameter for: NC - CQ Could not find bond parameter for: N2 - H Could not find bond parameter for: N2 - H Could not find bond parameter for: CA - N2 Could not find bond parameter for: CA - NC Could not find bond parameter for: CB - CA Could not find bond parameter for: CB - CB Could not find bond parameter for: NB - CB Could not find bond parameter for: CK - H5 Could not find bond parameter for: CK - NB Could not find bond parameter for: N* - CK Could not find bond parameter for: N* - CB Could not find bond parameter for: CT - H2 Could not find bond parameter for: CT - N* Could not find bond parameter for: CT - CT Could not find bond parameter for: OS - CT Could not find bond parameter for: CT - H1 Could not find bond parameter for: CT - OS Could not find bond parameter for: CT - CT Could not find bond parameter for: CI - H1 Could not find bond parameter for: CI - H1 Could not find bond parameter for: CI - CT Could not find bond parameter for: OH - CI Could not find bond parameter for: HO - OH Could not find bond parameter for: OH - HO Could not find bond parameter for: OH - HO Could not find bond parameter for: CT - H1 Could not find bond parameter for: CT - OH Could not find bond parameter for: CT - H1 Could not find bond parameter for: CT - CT Could not find bond parameter for: CT - OH Could not find bond parameter for: NC - CB Could not find bond parameter for: CQ - H5 Could not find bond parameter for: CQ - NC Could not find bond parameter for: NC - CQ Could not find bond parameter for: N2 - H Could not find bond parameter for: N2 - H Could not find bond parameter for: CA - N2 Could not find bond parameter for: CA - NC Could not find bond parameter for: CB - CA Could not find bond parameter for: CB - CB Could not find bond parameter for: NB - CB Could not find bond parameter for: CK - H5 Could not find bond parameter for: CK - NB Could not find bond parameter for: N* - CK Could not find bond parameter for: N* - CB Could not find bond parameter for: CT - H2 Could not find bond parameter for: CT - N* Could not find bond parameter for: CT - CT Could not find bond parameter for: OS - CT Could not find bond parameter for: CT - H1 Could not find bond parameter for: CT - OS Could not find bond parameter for: CT - CT Could not find bond parameter for: CI - H1 Could not find bond parameter for: CI - H1 Could not find bond parameter for: CI - CT Could not find bond parameter for: OS - CI Could not find bond parameter for: P - O2 Could not find bond parameter for: P - O2 Could not find bond parameter for: P - OS Checking for angle parameters. Could not find angle parameter: OS - P - O2 Could not find angle parameter: OS - P - O2 Could not find angle parameter: OS - P - OS Could not find angle parameter: H1 - CT - OH Could not find angle parameter: CT - CT - OS Could not find angle parameter: CT - OH - HO Could not find angle parameter: H1 - CT - CT Could not find angle parameter: H1 - CT - OS Could not find angle parameter: CT - CT - H1 Could not find angle parameter: CT - CT - OH Could not find angle parameter: CT - OS - P Could not find angle parameter: H5 - CQ - NC Could not find angle parameter: CQ - NC - CB Could not find angle parameter: NC - CQ - H5 Could not find angle parameter: NC - CQ - NC Could not find angle parameter: H - N2 - H Could not find angle parameter: N2 - CA - NC Could not find angle parameter: CA - CB - CB Could not find angle parameter: CA - N2 - H Could not find angle parameter: CA - N2 - H Could not find angle parameter: CA - NC - CQ Could not find angle parameter: CB - CA - N2 Could not find angle parameter: CB - CA - NC Could not find angle parameter: CB - CB - NC Could not find angle parameter: NB - CB - CA Could not find angle parameter: NB - CB - CB Could not find angle parameter: H5 - CK - NB Could not find angle parameter: CK - N* - CB Could not find angle parameter: CK - NB - CB Could not find angle parameter: N* - CT - CT Could not find angle parameter: N* - CK - H5 Could not find angle parameter: N* - CK - NB Could not find angle parameter: N* - CB - CB Could not find angle parameter: N* - CB - NC Could not find angle parameter: H2 - CT - N* Could not find angle parameter: H2 - CT - CT Could not find angle parameter: CT - N* - CK Could not find angle parameter: CT - N* - CB Could not find angle parameter: CT - CT - CT Could not find angle parameter: CT - CT - H1 Could not find angle parameter: CT - CT - OH Could not find angle parameter: OS - CT - CT Could not find angle parameter: OS - CT - H2 Could not find angle parameter: OS - CT - N* Could not find angle parameter: OS - CT - CT Could not find angle parameter: H1 - CT - OS Could not find angle parameter: H1 - CT - CT Could not find angle parameter: CT - OS - CT Could not find angle parameter: CT - CT - H1 Could not find angle parameter: CT - CT - CT Could not find angle parameter: CT - CT - OS Could not find angle parameter: H1 - CI - CT Could not find angle parameter: H1 - CI - H1 Could not find angle parameter: H1 - CI - CT Could not find angle parameter: CI - CT - H1 Could not find angle parameter: CI - CT - OS Could not find angle parameter: CI - CT - CT Could not find angle parameter: OH - CI - H1 Could not find angle parameter: OH - CI - H1 Could not find angle parameter: OH - CI - CT Could not find angle parameter: HO - OH - CI Could not find angle parameter: H1 - CT - OH Could not find angle parameter: CT - CT - OH Could not find angle parameter: CT - OH - HO Could not find angle parameter: H1 - CT - CT Could not find angle parameter: H1 - CT - OH Could not find angle parameter: CT - CT - H1 Could not find angle parameter: CT - CT - OH Could not find angle parameter: CT - OH - HO Could not find angle parameter: H5 - CQ - NC Could not find angle parameter: CQ - NC - CB Could not find angle parameter: NC - CQ - H5 Could not find angle parameter: NC - CQ - NC Could not find angle parameter: H - N2 - H Could not find angle parameter: N2 - CA - NC Could not find angle parameter: CA - CB - CB Could not find angle parameter: CA - N2 - H Could not find angle parameter: CA - N2 - H Could not find angle parameter: CA - NC - CQ Could not find angle parameter: CB - CA - N2 Could not find angle parameter: CB - CA - NC Could not find angle parameter: CB - CB - NC Could not find angle parameter: NB - CB - CA Could not find angle parameter: NB - CB - CB Could not find angle parameter: H5 - CK - NB Could not find angle parameter: CK - N* - CB Could not find angle parameter: CK - NB - CB Could not find angle parameter: N* - CT - CT Could not find angle parameter: N* - CK - H5 Could not find angle parameter: N* - CK - NB Could not find angle parameter: N* - CB - CB Could not find angle parameter: N* - CB - NC Could not find angle parameter: H2 - CT - N* Could not find angle parameter: H2 - CT - CT Could not find angle parameter: CT - N* - CK Could not find angle parameter: CT - N* - CB Could not find angle parameter: CT - CT - CT Could not find angle parameter: CT - CT - H1 Could not find angle parameter: CT - CT - OH Could not find angle parameter: OS - CT - CT Could not find angle parameter: OS - CT - H2 Could not find angle parameter: OS - CT - N* Could not find angle parameter: OS - CT - CT Could not find angle parameter: H1 - CT - OS Could not find angle parameter: H1 - CT - CT Could not find angle parameter: CT - OS - CT Could not find angle parameter: CT - CT - H1 Could not find angle parameter: CT - CT - CT Could not find angle parameter: CT - CT - OH Could not find angle parameter: H1 - CI - CT Could not find angle parameter: H1 - CI - H1 Could not find angle parameter: H1 - CI - CT Could not find angle parameter: CI - CT - H1 Could not find angle parameter: CI - CT - OS Could not find angle parameter: CI - CT - CT Could not find angle parameter: OS - CI - H1 Could not find angle parameter: OS - CI - H1 Could not find angle parameter: OS - CI - CT Could not find angle parameter: O2 - P - OS Could not find angle parameter: O2 - P - O2 Could not find angle parameter: O2 - P - OS Could not find angle parameter: P - OS - CI There are missing parameters. check: Warnings: 2 Unit is OK. Writing pdb file: init.pdb Quit