-I: Adding /home/hungn/BioMed/AMBER24/ORG/dat/leap/prep to search path. -I: Adding /home/hungn/BioMed/AMBER24/ORG/dat/leap/lib to search path. -I: Adding /home/hungn/BioMed/AMBER24/ORG/dat/leap/parm to search path. -I: Adding /home/hungn/BioMed/AMBER24/ORG/dat/leap/cmd to search path. -s: Ignoring all leaprc startup files. -f: Source MetalAA1_metal_tleap.in. Welcome to LEaP! Sourcing: ./MetalAA1_metal_tleap.in ----- Source: /home/hungn/BioMed/AMBER24/ORG/dat/leap/cmd/leaprc.protein.ff14SB ----- Source of /home/hungn/BioMed/AMBER24/ORG/dat/leap/cmd/leaprc.protein.ff14SB done Log file: ./leap.log Loading parameters: /home/hungn/BioMed/AMBER24/ORG/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA Loading parameters: /home/hungn/BioMed/AMBER24/ORG/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters Loading library: /home/hungn/BioMed/AMBER24/ORG/dat/leap/lib/amino12.lib Loading library: /home/hungn/BioMed/AMBER24/ORG/dat/leap/lib/aminoct12.lib Loading library: /home/hungn/BioMed/AMBER24/ORG/dat/leap/lib/aminont12.lib ----- Source: /home/hungn/BioMed/AMBER24/ORG/dat/leap/cmd/leaprc.gaff2 ----- Source of /home/hungn/BioMed/AMBER24/ORG/dat/leap/cmd/leaprc.gaff2 done Log file: ./leap.log Loading parameters: /home/hungn/BioMed/AMBER24/ORG/dat/leap/parm/gaff2.dat Reading title: AMBER General Force Field for organic molecules (Version 2.2.20, March 2021) ----- Source: /home/hungn/BioMed/AMBER24/ORG/dat/leap/cmd/leaprc.water.tip3p ----- Source of /home/hungn/BioMed/AMBER24/ORG/dat/leap/cmd/leaprc.water.tip3p done Loading library: /home/hungn/BioMed/AMBER24/ORG/dat/leap/lib/atomic_ions.lib Loading library: /home/hungn/BioMed/AMBER24/ORG/dat/leap/lib/solvents.lib Loading parameters: /home/hungn/BioMed/AMBER24/ORG/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/hungn/BioMed/AMBER24/ORG/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/hungn/BioMed/AMBER24/ORG/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/hungn/BioMed/AMBER24/ORG/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 Mol2 file: ./CM1.mol2 Reading MOLECULE named CM1 Loading Mol2 file: ./HM1.mol2 Reading MOLECULE named HM1 Loading Mol2 file: ./FE1.mol2 Reading MOLECULE named FE1 Loading parameters: /home/hungn/BioMed/AMBER24/ORG/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: ./MetalAA1_metal.frcmod Reading force field modification type file (frcmod) Reading title: REMARK MAPLE MetalAA generated metal-site frcmod Loading PDB file: ./MetalAA1_metal_tleap.pdb /home/hungn/BioMed/AMBER24/ORG/bin/teLeap: Warning! One sided connection. Residue (CM1) missing connect0 atom. /home/hungn/BioMed/AMBER24/ORG/bin/teLeap: Warning! One sided connection. Residue (default_name) missing connect1 atom. total atoms in file: 7440 Writing pdb file: MetalAA1_metal_tleap_dry.pdb /home/hungn/BioMed/AMBER24/ORG/bin/teLeap: Warning! Converting N-terminal residue name to PDB format: NTHR -> THR /home/hungn/BioMed/AMBER24/ORG/bin/teLeap: Warning! Converting C-terminal residue name to PDB format: CSER -> SER Checking Unit. /home/hungn/BioMed/AMBER24/ORG/bin/teLeap: Warning! The unperturbed charge of the unit (-11.000000) is not zero. /home/hungn/BioMed/AMBER24/ORG/bin/teLeap: Note. Ignoring the warning from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 1483 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CM1 1 CSER 1 HM1 1 NTHR 1 ) (no restraints) Solute vdw bounding box: 68.422 62.787 72.413 Total bounding box for atom centers: 88.422 82.787 92.413 Solvent unit box: 18.774 18.774 18.774 Total vdw box size: 91.309 85.784 95.594 angstroms. Volume: 748772.895 A^3 Total mass 378201.556 amu, Density 0.839 g/cc Added 18052 residues. 11 Na+ ions required to neutralize. Adding 11 counter ions to "mol" using 1A grid Grid extends from solute vdw + 3.13 to 9.13 Resolution: 1.00 Angstrom. Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Na+ in mol at (-12.57, 10.39, -11.71). (Replacing solvent molecule) Placed Na+ in mol at (-11.87, -3.03, 32.93). (Replacing solvent molecule) Placed Na+ in mol at (-8.52, -25.92, 6.11). (Replacing solvent molecule) Placed Na+ in mol at (-8.22, 27.35, 11.39). (Replacing solvent molecule) Placed Na+ in mol at (-8.63, 6.41, -19.65). (Replacing solvent molecule) Placed Na+ in mol at (-10.44, -22.35, -11.28). (Replacing solvent molecule) Placed Na+ in mol at (-1.86, 11.71, -36.33). (Replacing solvent molecule) Placed Na+ in mol at (-29.30, 1.55, -8.85). (Replacing solvent molecule) Placed Na+ in mol at (-5.15, 24.02, 1.41). (Replacing solvent molecule) Placed Na+ in mol at (-8.37, -18.38, 7.85). (Replacing solvent molecule) Placed Na+ in mol at (15.71, -18.62, -20.30). Done adding ions. /home/hungn/BioMed/AMBER24/ORG/bin/teLeap: Warning! addIons: 1st Ion & target unit have charges of the same sign: unit charge = -5.32907e-15; ion1 charge = -1; can't neutralize. Writing pdb file: MetalAA1_metal_tleap_solvated.pdb printing CRYST1 record to PDB file with box info /home/hungn/BioMed/AMBER24/ORG/bin/teLeap: Warning! Converting N-terminal residue name to PDB format: NTHR -> THR /home/hungn/BioMed/AMBER24/ORG/bin/teLeap: Warning! Converting C-terminal residue name to PDB format: CSER -> SER Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 1483 improper torsions applied Building H-Bond parameters. Incorporating Non-Bonded adjustments. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected CM1 1 CSER 1 HM1 1 NTHR 1 WAT 18041 ) (no restraints) Quit Exiting LEaP: Errors = 0; Warnings = 8; Notes = 1.