-I: Adding /home/xxxx/sources/amber22/dat/leap/prep to search path. -I: Adding /home/xxxx/sources/amber22/dat/leap/lib to search path. -I: Adding /home/xxxx/sources/amber22/dat/leap/parm to search path. -I: Adding /home/xxxx/sources/amber22/dat/leap/cmd to search path. -s: Ignoring all leaprc startup files. -f: Source tleap_ZAFF.in. Welcome to LEaP! Sourcing: ./tleap_ZAFF.in ----- Source: /home/xxxx/sources/amber22/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /home/xxxx/sources/amber22/dat/leap/cmd/leaprc.protein.ff14SB done Log file: ./leap.log Loading parameters: /home/xxxx/sources/amber22/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA Loading parameters: /home/xxxx/sources/amber22/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters Loading library: /home/xxxx/sources/amber22/dat/leap/lib/amino12.lib Loading library: /home/xxxx/sources/amber22/dat/leap/lib/aminoct12.lib Loading library: /home/xxxx/sources/amber22/dat/leap/lib/aminont12.lib ----- Source: /home/xxxx/sources/amber22/dat/leap/cmd/leaprc.water.tip3p ----- Source of /home/xxxx/sources/amber22/dat/leap/cmd/leaprc.water.tip3p done Loading library: /home/xxxx/sources/amber22/dat/leap/lib/atomic_ions.lib Loading library: /home/xxxx/sources/amber22/dat/leap/lib/solvents.lib Loading parameters: /home/xxxx/sources/amber22/dat/leap/parm/frcmod.tip3p Reading force field modification type file (frcmod) Reading title: This is the additional/replacement parameter set for TIP3P water Loading parameters: /home/xxxx/sources/amber22/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) Loading parameters: /home/xxxx/sources/amber22/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) Loading parameters: /home/xxxx/sources/amber22/dat/leap/parm/frcmod.ions234lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set) Loading parameters: /home/xxxx/sources/amber22/dat/leap/parm/frcmod.ions1lm_126_tip3p Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set) Loading Prep file: ./ZAFF.prep Loading parameters: ./ZAFF.frcmod Reading force field modification type file (frcmod) Reading title: ZAFF parameter set created by MTK++/MCPB Loading PDB file: ./example_ZAFF.pdb total atoms in file: 4171 Leap added 4049 missing atoms according to residue templates: 4049 H / lone pairs Writing pdb file: example_ZAFF_dry.pdb /home/xxxx/sources/amber22/bin/teLeap: Warning! Converting N-terminal residue name to PDB format: NGLU -> GLU /home/xxxx/sources/amber22/bin/teLeap: Warning! Converting C-terminal residue name to PDB format: CPHE -> PHE Checking Unit. /home/xxxx/sources/amber22/bin/teLeap: Warning! The unperturbed charge of the unit (8.999980) is not zero. /home/xxxx/sources/amber22/bin/teLeap: Note. Ignoring the warning from Unit Checking. Building topology. Building atom parameters. Building bond parameters. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find bond parameter for atom types: NA - ZN for atom ND1 at position 107.800000, 124.004000, 97.269000 and atom ZN at position 109.016000, 125.355000, 97.593000. Building angle parameters. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find angle parameter for atom types: N3 - ZN - NA for atom NE2 at position 108.871000, 126.230000, 99.160000, atom ZN at position 109.016000, 125.355000, 97.593000, and atom ND1 at position 107.800000, 124.004000, 97.269000. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find angle parameter for atom types: S4 - ZN - NA for atom SG at position 108.355000, 126.897000, 96.003000, atom ZN at position 109.016000, 125.355000, 97.593000, and atom ND1 at position 107.800000, 124.004000, 97.269000. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find angle parameter for atom types: CR - NA - ZN for atom CE1 at position 108.168000, 123.094000, 96.344000, atom ND1 at position 107.800000, 124.004000, 97.269000, and atom ZN at position 109.016000, 125.355000, 97.593000. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find angle parameter for atom types: H - NA - ZN for atom HD1 at position 108.414658, 124.649154, 97.744470, atom ND1 at position 107.800000, 124.004000, 97.269000, and atom ZN at position 109.016000, 125.355000, 97.593000. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find angle parameter for atom types: NA - ZN - S4 for atom ND1 at position 107.800000, 124.004000, 97.269000, atom ZN at position 109.016000, 125.355000, 97.593000, and atom SG at position 111.215000, 124.515000, 97.498000. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find angle parameter for atom types: CC - NA - ZN for atom CG at position 106.413000, 123.849000, 97.410000, atom ND1 at position 107.800000, 124.004000, 97.269000, and atom ZN at position 109.016000, 125.355000, 97.593000. Building proper torsion parameters. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: CV-N3-ZN-NA for atom CD2 at position 109.706000, 126.306000, 100.281000, atom NE2 at position 108.871000, 126.230000, 99.160000, atom ZN at position 109.016000, 125.355000, 97.593000, and atom ND1 at position 107.800000, 124.004000, 97.269000. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: N3-ZN-NA-CC for atom NE2 at position 108.871000, 126.230000, 99.160000, atom ZN at position 109.016000, 125.355000, 97.593000, atom ND1 at position 107.800000, 124.004000, 97.269000, and atom CG at position 106.413000, 123.849000, 97.410000. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: N3-ZN-NA-H for atom NE2 at position 108.871000, 126.230000, 99.160000, atom ZN at position 109.016000, 125.355000, 97.593000, atom ND1 at position 107.800000, 124.004000, 97.269000, and atom HD1 at position 108.414658, 124.649154, 97.744470. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: N3-ZN-NA-CR for atom NE2 at position 108.871000, 126.230000, 99.160000, atom ZN at position 109.016000, 125.355000, 97.593000, atom ND1 at position 107.800000, 124.004000, 97.269000, and atom CE1 at position 108.168000, 123.094000, 96.344000. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: CR-N3-ZN-NA for atom CE1 at position 107.931000, 127.180000, 99.341000, atom NE2 at position 108.871000, 126.230000, 99.160000, atom ZN at position 109.016000, 125.355000, 97.593000, and atom ND1 at position 107.800000, 124.004000, 97.269000. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: S4-ZN-NA-CC for atom SG at position 108.355000, 126.897000, 96.003000, atom ZN at position 109.016000, 125.355000, 97.593000, atom ND1 at position 107.800000, 124.004000, 97.269000, and atom CG at position 106.413000, 123.849000, 97.410000. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: S4-ZN-NA-H for atom SG at position 108.355000, 126.897000, 96.003000, atom ZN at position 109.016000, 125.355000, 97.593000, atom ND1 at position 107.800000, 124.004000, 97.269000, and atom HD1 at position 108.414658, 124.649154, 97.744470. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: S4-ZN-NA-CR for atom SG at position 108.355000, 126.897000, 96.003000, atom ZN at position 109.016000, 125.355000, 97.593000, atom ND1 at position 107.800000, 124.004000, 97.269000, and atom CE1 at position 108.168000, 123.094000, 96.344000. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: CT-S4-ZN-NA for atom CB at position 109.641000, 128.069000, 96.506000, atom SG at position 108.355000, 126.897000, 96.003000, atom ZN at position 109.016000, 125.355000, 97.593000, and atom ND1 at position 107.800000, 124.004000, 97.269000. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: CR-NA-ZN-S4 for atom CE1 at position 108.168000, 123.094000, 96.344000, atom ND1 at position 107.800000, 124.004000, 97.269000, atom ZN at position 109.016000, 125.355000, 97.593000, and atom SG at position 111.215000, 124.515000, 97.498000. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: H-NA-ZN-S4 for atom HD1 at position 108.414658, 124.649154, 97.744470, atom ND1 at position 107.800000, 124.004000, 97.269000, atom ZN at position 109.016000, 125.355000, 97.593000, and atom SG at position 111.215000, 124.515000, 97.498000. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: NA-ZN-S4-CT for atom ND1 at position 107.800000, 124.004000, 97.269000, atom ZN at position 109.016000, 125.355000, 97.593000, atom SG at position 111.215000, 124.515000, 97.498000, and atom CB at position 111.230000, 123.106000, 98.641000. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: CC-NA-ZN-S4 for atom CG at position 106.413000, 123.849000, 97.410000, atom ND1 at position 107.800000, 124.004000, 97.269000, atom ZN at position 109.016000, 125.355000, 97.593000, and atom SG at position 111.215000, 124.515000, 97.498000. Building improper torsion parameters. old PREP-specified impropers: : -M CA N H : CA +M C O : CG CE1 ND1 HD1 : CG NE2 CD2 HD2 : ND1 NE2 CE1 HE1 : ND1 CD2 CG CB : -M CA N HN : CA +M C O : -M CA N H : CA +M C O : CG CE1 ND1 HD1 : CG NE2 CD2 HD2 : ND1 NE2 CE1 HE1 : ND1 CD2 CG CB : -M CA N HN : CA +M C O total 1765 improper torsions applied 16 improper torsions in old prep form Building H-Bond parameters. Incorporating Non-Bonded adjustments. /home/xxxx/sources/amber22/bin/teLeap: Warning! Parameter file was not saved. Solute vdw bounding box: 62.238 68.081 117.085 Total bounding box for atom centers: 82.238 88.081 137.085 Solvent unit box: 18.774 18.774 18.774 Total vdw box size: 85.235 90.583 140.127 angstroms. Volume: 1081893.389 A^3 Total mass 555038.258 amu, Density 0.852 g/cc Added 27506 residues. Total unperturbed charge: 8.999980 Total perturbed charge: 8.999980 9 CL ions required to neutralize. Adding 9 counter ions to "mol" using 1A grid Grid extends from solute vdw + 4.85 to 10.85 Resolution: 1.00 Angstrom. Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed CL in mol at (-6.22, 7.86, 18.21). (Replacing solvent molecule) Placed CL in mol at (-27.01, -10.51, 25.28). (Replacing solvent molecule) Placed CL in mol at (-21.79, 7.79, 33.64). (Replacing solvent molecule) Placed CL in mol at (-21.82, -7.64, 5.60). (Replacing solvent molecule) Placed CL in mol at (-1.07, -24.56, -11.78). (Replacing solvent molecule) Placed CL in mol at (-12.57, 13.03, -33.58). (Replacing solvent molecule) Placed CL in mol at (20.24, -0.78, -22.42). (Replacing solvent molecule) Placed CL in mol at (5.66, -14.82, 24.42). (Replacing solvent molecule) Placed CL in mol at (5.30, -19.36, -29.88). Done adding ions. Writing pdb file: example_ZAFF_solv.pdb printing CRYST1 record to PDB file with box info /home/xxxx/sources/amber22/bin/teLeap: Warning! Converting N-terminal residue name to PDB format: NGLU -> GLU /home/xxxx/sources/amber22/bin/teLeap: Warning! Converting C-terminal residue name to PDB format: CPHE -> PHE Checking Unit. Building topology. Building atom parameters. Building bond parameters. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find bond parameter for atom types: NA - ZN for atom ND1 at position -7.302631, 8.675131, -3.184384 and atom ZN at position -6.086631, 10.026131, -2.860384. Building angle parameters. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find angle parameter for atom types: N3 - ZN - NA for atom NE2 at position -6.231631, 10.901131, -1.293384, atom ZN at position -6.086631, 10.026131, -2.860384, and atom ND1 at position -7.302631, 8.675131, -3.184384. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find angle parameter for atom types: S4 - ZN - NA for atom SG at position -6.747631, 11.568131, -4.450384, atom ZN at position -6.086631, 10.026131, -2.860384, and atom ND1 at position -7.302631, 8.675131, -3.184384. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find angle parameter for atom types: CR - NA - ZN for atom CE1 at position -6.934631, 7.765131, -4.109384, atom ND1 at position -7.302631, 8.675131, -3.184384, and atom ZN at position -6.086631, 10.026131, -2.860384. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find angle parameter for atom types: H - NA - ZN for atom HD1 at position -6.687973, 9.320285, -2.708914, atom ND1 at position -7.302631, 8.675131, -3.184384, and atom ZN at position -6.086631, 10.026131, -2.860384. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find angle parameter for atom types: NA - ZN - S4 for atom ND1 at position -7.302631, 8.675131, -3.184384, atom ZN at position -6.086631, 10.026131, -2.860384, and atom SG at position -3.887631, 9.186131, -2.955384. /home/xxxx/sources/amber22/bin/teLeap: Error! Could not find angle parameter for atom types: CC - NA - ZN for atom CG at position -8.689631, 8.520131, -3.043384, atom ND1 at position -7.302631, 8.675131, -3.184384, and atom ZN at position -6.086631, 10.026131, -2.860384. Building proper torsion parameters. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: CV-N3-ZN-NA for atom CD2 at position -5.396631, 10.977131, -0.172384, atom NE2 at position -6.231631, 10.901131, -1.293384, atom ZN at position -6.086631, 10.026131, -2.860384, and atom ND1 at position -7.302631, 8.675131, -3.184384. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: N3-ZN-NA-CC for atom NE2 at position -6.231631, 10.901131, -1.293384, atom ZN at position -6.086631, 10.026131, -2.860384, atom ND1 at position -7.302631, 8.675131, -3.184384, and atom CG at position -8.689631, 8.520131, -3.043384. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: N3-ZN-NA-H for atom NE2 at position -6.231631, 10.901131, -1.293384, atom ZN at position -6.086631, 10.026131, -2.860384, atom ND1 at position -7.302631, 8.675131, -3.184384, and atom HD1 at position -6.687973, 9.320285, -2.708914. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: N3-ZN-NA-CR for atom NE2 at position -6.231631, 10.901131, -1.293384, atom ZN at position -6.086631, 10.026131, -2.860384, atom ND1 at position -7.302631, 8.675131, -3.184384, and atom CE1 at position -6.934631, 7.765131, -4.109384. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: CR-N3-ZN-NA for atom CE1 at position -7.171631, 11.851131, -1.112384, atom NE2 at position -6.231631, 10.901131, -1.293384, atom ZN at position -6.086631, 10.026131, -2.860384, and atom ND1 at position -7.302631, 8.675131, -3.184384. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: S4-ZN-NA-CC for atom SG at position -6.747631, 11.568131, -4.450384, atom ZN at position -6.086631, 10.026131, -2.860384, atom ND1 at position -7.302631, 8.675131, -3.184384, and atom CG at position -8.689631, 8.520131, -3.043384. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: S4-ZN-NA-H for atom SG at position -6.747631, 11.568131, -4.450384, atom ZN at position -6.086631, 10.026131, -2.860384, atom ND1 at position -7.302631, 8.675131, -3.184384, and atom HD1 at position -6.687973, 9.320285, -2.708914. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: S4-ZN-NA-CR for atom SG at position -6.747631, 11.568131, -4.450384, atom ZN at position -6.086631, 10.026131, -2.860384, atom ND1 at position -7.302631, 8.675131, -3.184384, and atom CE1 at position -6.934631, 7.765131, -4.109384. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: CT-S4-ZN-NA for atom CB at position -5.461631, 12.740131, -3.947384, atom SG at position -6.747631, 11.568131, -4.450384, atom ZN at position -6.086631, 10.026131, -2.860384, and atom ND1 at position -7.302631, 8.675131, -3.184384. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: CR-NA-ZN-S4 for atom CE1 at position -6.934631, 7.765131, -4.109384, atom ND1 at position -7.302631, 8.675131, -3.184384, atom ZN at position -6.086631, 10.026131, -2.860384, and atom SG at position -3.887631, 9.186131, -2.955384. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: H-NA-ZN-S4 for atom HD1 at position -6.687973, 9.320285, -2.708914, atom ND1 at position -7.302631, 8.675131, -3.184384, atom ZN at position -6.086631, 10.026131, -2.860384, and atom SG at position -3.887631, 9.186131, -2.955384. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: NA-ZN-S4-CT for atom ND1 at position -7.302631, 8.675131, -3.184384, atom ZN at position -6.086631, 10.026131, -2.860384, atom SG at position -3.887631, 9.186131, -2.955384, and atom CB at position -3.872631, 7.777131, -1.812384. /home/xxxx/sources/amber22/bin/teLeap: Error! ** No torsion terms for atom types: CC-NA-ZN-S4 for atom CG at position -8.689631, 8.520131, -3.043384, atom ND1 at position -7.302631, 8.675131, -3.184384, atom ZN at position -6.086631, 10.026131, -2.860384, and atom SG at position -3.887631, 9.186131, -2.955384. Building improper torsion parameters. old PREP-specified impropers: : -M CA N H : CA +M C O : CG CE1 ND1 HD1 : CG NE2 CD2 HD2 : ND1 NE2 CE1 HE1 : ND1 CD2 CG CB : -M CA N HN : CA +M C O : -M CA N H : CA +M C O : CG CE1 ND1 HD1 : CG NE2 CD2 HD2 : ND1 NE2 CE1 HE1 : ND1 CD2 CG CB : -M CA N HN : CA +M C O total 1765 improper torsions applied 16 improper torsions in old prep form Building H-Bond parameters. Incorporating Non-Bonded adjustments. /home/xxxx/sources/amber22/bin/teLeap: Warning! Parameter file was not saved. Quit Exiting LEaP: Errors = 40; Warnings = 7; Notes = 1.