Sourcing: ./Initial.in ----- Source: /home/horace/mbdxfsi2/amber9//dat/leap/cmd/leaprc.ff03 ----- Source of /home/horace/mbdxfsi2/amber9//dat/leap/cmd/leaprc.ff03 done Log file: ./leap.log Loading parameters: /home/horace/mbdxfsi2/amber9//dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 Loading parameters: /home/horace/mbdxfsi2/amber9//dat/leap/parm/frcmod.ff03 Reading force field modification type file (frcmod) Reading title: Duan et al ff03 phi psi torsions Loading library: /home/horace/mbdxfsi2/amber9//dat/leap/lib/ions94.lib Loading library: /home/horace/mbdxfsi2/amber9//dat/leap/lib/solvents.lib Loading library: /home/horace/mbdxfsi2/amber9//dat/leap/lib/all_nucleic94.lib Loading library: /home/horace/mbdxfsi2/amber9//dat/leap/lib/all_aminoct94.lib Loading library: /home/horace/mbdxfsi2/amber9//dat/leap/lib/all_aminont94.lib Loading library: /home/horace/mbdxfsi2/amber9//dat/leap/lib/all_amino03.lib Loading parameters: /home/horace/mbdxfsi2/amber9//dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) Loading Prep file: ./PD_prep.prepin Loading PDB file: ./Mol2-PDB.pdb +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C13-C14-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C12-C13-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C11-C12-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C10-C11-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C9-C10-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C9-C14-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C8-C9-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C4-C8-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C5-C4-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C6-C5-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C1-C6-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C2-C1-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C3-C2-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C3-C4-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C7-C3-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C7-C10-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C13-C14-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C12-C13-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C11-C12-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C10-C11-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C9-C10-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C9-C14-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C8-C9-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C4-C8-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C5-C4-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C6-C5-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C1-C6-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C2-C1-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C3-C2-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C3-C4-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C7-C3-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported +---Tried to superimpose torsions for: *-C7-C10-* +--- With Sp0 - Sp0 +--- Sp0 probably means a new atom type is involved +--- which needs to be added via addAtomTypes Bond: maximum coordination exceeded on .R.A

-- setting atoms pert=true overrides default limits ATOMS NOT BONDED: .R.A

.R.A !FATAL ERROR---------------------------------------- !FATAL: In file [atom.c], line 444 !FATAL: Message: bondAtomProblem found ! !ABORTING.