-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 NCAA1_ncaa_tleap.in. Welcome to LEaP! Sourcing: ./NCAA1_ncaa_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 Prep file: ./HF1_maple.prepin Loading parameters: ./HF1_maple.frcmod Reading force field modification type file (frcmod) Reading title: REMARK MAPLE ncaa refined frcmod Loading PDB file: ./NCAA1_ncaa_tleap.pdb total atoms in file: 8267 Checking 'mol'.... /home/hungn/BioMed/AMBER24/ORG/bin/teLeap: Warning! The unperturbed charge of the unit (-4.000000) is not zero. Checking parameters for unit 'mol'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 1 Unit is OK. Total unperturbed charge: -4.000000 Total perturbed charge: -4.000000 Solute vdw bounding box: 87.949 63.372 67.525 Total bounding box for atom centers: 107.949 83.372 87.525 Solvent unit box: 18.774 18.774 18.774 Total vdw box size: 111.102 86.834 90.552 angstroms. Volume: 873595.949 A^3 Total mass 440364.502 amu, Density 0.837 g/cc Added 21157 residues. 4 Na+ ions required to neutralize. Adding 4 counter ions to "mol" using 1A grid Grid extends from solute vdw + 1.37 to 7.44 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 (43.82, 2.09, 2.86). (Replacing solvent molecule) Placed Na+ in mol at (7.75, -3.34, -22.64). (Replacing solvent molecule) Placed Na+ in mol at (35.65, 6.71, 0.10). (Replacing solvent molecule) Placed Na+ in mol at (-24.09, 5.95, 30.69). Done adding ions. 0.000000 0 1 0 0 Cl- ion required to neutralize. Adding 0 counter ions to "mol" using 1A grid Writing pdb file: NCAA1_ncaa_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: CLEU -> LEU Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. old PREP-specified impropers: : -M CA N H : C3 C5 C4 N2 : C30 C4 N2 C6 : H6 N2 C6 N3 : C4 H5 C5 N3 : C30 C26 C28 C31 : C27 C28 C26 C24 : C26 C23 C24 H9 : C24 C32 C23 N9 : C17 C33 C20 N9 : C20 N7 C17 O15 : C17 C13 N7 H8 : N5 N7 C13 O11 : C20 N13 C33 N5 : C11 C32 N13 C33 : C12 C18 N12 C29 : C21 N12 C18 N8 : H20 N8 C14 N6 : C21 N6 C25 N10 : C25 H30 N10 H31 : C18 C25 C21 N11 : H32 N12 C29 N11 : C23 C31 C32 N13 : C28 C32 C31 H10 : +M CA C O total 1736 improper torsions applied 25 improper torsions in old prep form 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 CLEU 1 NTHR 1 WAT 21153 ) (no restraints) Quit Exiting LEaP: Errors = 0; Warnings = 3; Notes = 0.