log started: Wed Mar 26 11:17:54 2025 Log file: ./leap.log >> # >> # ----- leaprc for loading the ff19SB force field >> # ----- NOTE: this is designed for PDB format 3! >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "H" "H" "sp3" } >> { "HO" "H" "sp3" } >> { "HS" "H" "sp3" } >> { "H1" "H" "sp3" } >> { "H2" "H" "sp3" } >> { "H3" "H" "sp3" } >> { "H4" "H" "sp3" } >> { "H5" "H" "sp3" } >> { "HW" "H" "sp3" } >> { "HC" "H" "sp3" } >> { "HA" "H" "sp3" } >> { "HP" "H" "sp3" } >> { "HZ" "H" "sp3" } >> { "OH" "O" "sp3" } >> { "OS" "O" "sp3" } >> { "O" "O" "sp2" } >> { "O2" "O" "sp2" } >> { "OP" "O" "sp2" } >> { "OW" "O" "sp3" } >> { "CT" "C" "sp3" } >> { "CX" "C" "sp3" } >> { "XC" "C" "sp3" } >> { "C8" "C" "sp3" } >> { "2C" "C" "sp3" } >> { "3C" "C" "sp3" } >> { "CH" "C" "sp3" } >> { "CS" "C" "sp2" } >> { "C" "C" "sp2" } >> { "CO" "C" "sp2" } >> { "C*" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CB" "C" "sp2" } >> { "CC" "C" "sp2" } >> { "CN" "C" "sp2" } >> { "CM" "C" "sp2" } >> { "CK" "C" "sp2" } >> { "CQ" "C" "sp2" } >> { "CD" "C" "sp2" } >> { "C5" "C" "sp2" } >> { "C4" "C" "sp2" } >> { "CP" "C" "sp2" } >> { "CI" "C" "sp3" } >> { "CJ" "C" "sp2" } >> { "CW" "C" "sp2" } >> { "CV" "C" "sp2" } >> { "CR" "C" "sp2" } >> { "CA" "C" "sp2" } >> { "CY" "C" "sp2" } >> { "C0" "Ca" "sp3" } >> { "MG" "Mg" "sp3" } >> { "N" "N" "sp2" } >> { "NA" "N" "sp2" } >> { "N2" "N" "sp2" } >> { "N*" "N" "sp2" } >> { "NP" "N" "sp2" } >> { "NQ" "N" "sp2" } >> { "NB" "N" "sp2" } >> { "NC" "N" "sp2" } >> { "NT" "N" "sp3" } >> { "NY" "N" "sp2" } >> { "N3" "N" "sp3" } >> { "S" "S" "sp3" } >> { "SH" "S" "sp3" } >> { "P" "P" "sp3" } >> { "LP" "" "sp3" } >> { "EP" "" "sp3" } >> { "F" "F" "sp3" } >> { "Cl" "Cl" "sp3" } >> { "Br" "Br" "sp3" } >> { "I" "I" "sp3" } >> } >> # >> # Load the main parameter set. >> # >> set default cmap on >> parm19 = loadamberparams parm19.dat Loading parameters: /home/student/Structural_bioinformatics/amber20/dat/leap/parm/parm19.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA + ff19SB (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) >> frcmod19SB = loadamberparams frcmod.ff19SB Loading parameters: /home/student/Structural_bioinformatics/amber20/dat/leap/parm/frcmod.ff19SB Reading force field modification type file (frcmod) Reading title: ff19SB AA-specific backbone CMAPs for protein 07/25/2019 >> # >> # Load main chain and terminating amino acid libraries >> # >> loadOff amino19.lib Loading library: /home/student/Structural_bioinformatics/amber20/dat/leap/lib/amino19.lib Loading: ALA Loading: ARG Loading: ASH Loading: ASN Loading: ASP Loading: CYM Loading: CYS Loading: CYX Loading: GLH Loading: GLN Loading: GLU Loading: GLY Loading: HID Loading: HIE Loading: HIP Loading: HYP Loading: ILE Loading: LEU Loading: LYN Loading: LYS Loading: MET Loading: PHE Loading: PRO Loading: SER Loading: THR Loading: TRP Loading: TYR Loading: VAL >> loadOff aminoct12.lib Loading library: /home/student/Structural_bioinformatics/amber20/dat/leap/lib/aminoct12.lib Loading: CALA Loading: CARG Loading: CASN Loading: CASP Loading: CCYS Loading: CCYX Loading: CGLN Loading: CGLU Loading: CGLY Loading: CHID Loading: CHIE Loading: CHIP Loading: CHYP Loading: CILE Loading: CLEU Loading: CLYS Loading: CMET Loading: CPHE Loading: CPRO Loading: CSER Loading: CTHR Loading: CTRP Loading: CTYR Loading: CVAL Loading: NHE Loading: NME >> loadOff aminont12.lib Loading library: /home/student/Structural_bioinformatics/amber20/dat/leap/lib/aminont12.lib Loading: ACE Loading: NALA Loading: NARG Loading: NASN Loading: NASP Loading: NCYS Loading: NCYX Loading: NGLN Loading: NGLU Loading: NGLY Loading: NHID Loading: NHIE Loading: NHIP Loading: NILE Loading: NLEU Loading: NLYS Loading: NMET Loading: NPHE Loading: NPRO Loading: NSER Loading: NTHR Loading: NTRP Loading: NTYR Loading: NVAL >> >> # >> # Define the PDB name map for the amino acids >> # >> addPdbResMap { >> { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" } >> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } >> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } >> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } >> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } >> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } >> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } >> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } >> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } >> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } >> { 0 "HID" "NHID" } { 1 "HID" "CHID" } >> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } >> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } >> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } >> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } >> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } >> { 0 "MET" "NMET" } { 1 "MET" "CMET" } >> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } >> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } >> { 0 "SER" "NSER" } { 1 "SER" "CSER" } >> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } >> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } >> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } >> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } >> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } >> } >> >> # >> # assume that most often proteins use HIE >> # >> NHIS = NHIE >> HIS = HIE >> CHIS = CHIE > > source leaprc.water.opc ----- Source: /home/student/Structural_bioinformatics/amber20/dat/leap/cmd/leaprc.water.opc ----- Source of /home/student/Structural_bioinformatics/amber20/dat/leap/cmd/leaprc.water.opc done >> # >> # Load water and ions for OPC + Joung-Chetham monovalent ions for >> # tip4pew + Li/Merz highly charged ions (+2 to +4, 12-6 normal usage set) >> # for tip4pew >> # >> addAtomTypes { >> { "F-" "F" "sp3" } >> { "Cl-" "Cl" "sp3" } >> { "Br-" "Br" "sp3" } >> { "I-" "I" "sp3" } >> { "Li+" "Li" "sp3" } >> { "Na+" "Na" "sp3" } >> { "K+" "K" "sp3" } >> { "Rb+" "Rb" "sp3" } >> { "Cs+" "Cs" "sp3" } >> { "Mg+" "Mg" "sp3" } >> { "Tl+" "Tl" "sp3" } >> { "Cu+" "Cu" "sp3" } >> { "Ag+" "Ag" "sp3" } >> { "Be2+" "Be" "sp3" } >> { "Cu2+" "Cu" "sp3" } >> { "Ni2+" "Ni" "sp3" } >> { "Pt2+" "Pt" "sp3" } >> { "Zn2+" "Zn" "sp3" } >> { "Co2+" "Co" "sp3" } >> { "Pd2+" "Pd" "sp3" } >> { "Ag2+" "Ag" "sp3" } >> { "Cr2+" "Cr" "sp3" } >> { "Fe2+" "Fe" "sp3" } >> { "Mg2+" "Mg" "sp3" } >> { "V2+" "V" "sp3" } >> { "Mn2+" "Mn" "sp3" } >> { "Hg2+" "Hg" "sp3" } >> { "Cd2+" "Cd" "sp3" } >> { "Yb2+" "Yb" "sp3" } >> { "Ca2+" "Ca" "sp3" } >> { "Sn2+" "Sn" "sp3" } >> { "Pb2+" "Pb" "sp3" } >> { "Eu2+" "Eu" "sp3" } >> { "Sr2+" "Sr" "sp3" } >> { "Sm2+" "Sm" "sp3" } >> { "Ba2+" "Ba" "sp3" } >> { "Ra2+" "Ra" "sp3" } >> { "Al3+" "Al" "sp3" } >> { "Fe3+" "Fe" "sp3" } >> { "Cr3+" "Cr" "sp3" } >> { "In3+" "In" "sp3" } >> { "Tl3+" "Tl" "sp3" } >> { "Y3+" "Y" "sp3" } >> { "La3+" "La" "sp3" } >> { "Ce3+" "Ce" "sp3" } >> { "Pr3+" "Pr" "sp3" } >> { "Nd3+" "Nd" "sp3" } >> { "Sm3+" "Sm" "sp3" } >> { "Eu3+" "Eu" "sp3" } >> { "Gd3+" "Gd" "sp3" } >> { "Tb3+" "Tb" "sp3" } >> { "Dy3+" "Dy" "sp3" } >> { "Er3+" "Er" "sp3" } >> { "Tm3+" "Tm" "sp3" } >> { "Lu3+" "Lu" "sp3" } >> { "Hf4+" "Hf" "sp3" } >> { "Zr4+" "Zr" "sp3" } >> { "Ce4+" "Ce" "sp3" } >> { "U4+" "U" "sp3" } >> { "Pu4+" "Pu" "sp3" } >> { "Th4+" "Th" "sp3" } >> { "OW" "O" "sp3" } >> { "HW" "H" "sp3" } >> { "EP" "" "sp3" } >> } >> loadOff atomic_ions.lib Loading library: /home/student/Structural_bioinformatics/amber20/dat/leap/lib/atomic_ions.lib Loading: AG Loading: AL Loading: Ag Loading: BA Loading: BR Loading: Be Loading: CA Loading: CD Loading: CE Loading: CL Loading: CO Loading: CR Loading: CS Loading: CU Loading: CU1 Loading: Ce Loading: Cl- Loading: Cr Loading: Dy Loading: EU Loading: EU3 Loading: Er Loading: F Loading: FE Loading: FE2 Loading: GD3 Loading: H3O+ Loading: HE+ Loading: HG Loading: HZ+ Loading: Hf Loading: IN Loading: IOD Loading: K Loading: K+ Loading: LA Loading: LI Loading: LU Loading: MG Loading: MN Loading: NA Loading: NH4 Loading: NI Loading: Na+ Loading: Nd Loading: PB Loading: PD Loading: PR Loading: PT Loading: Pu Loading: RB Loading: Ra Loading: SM Loading: SR Loading: Sm Loading: Sn Loading: TB Loading: TL Loading: Th Loading: Tl Loading: Tm Loading: U4+ Loading: V2+ Loading: Y Loading: YB2 Loading: ZN Loading: Zr >> loadOff solvents.lib Loading library: /home/student/Structural_bioinformatics/amber20/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OP3 Loading: OPC Loading: OPC3BOX Loading: OPCBOX Loading: PL3 Loading: POL3BOX Loading: QSPCFWBOX Loading: SPC Loading: SPCBOX Loading: SPCFWBOX Loading: SPF Loading: SPG Loading: T4E Loading: TIP3PBOX Loading: TIP3PFBOX Loading: TIP4PBOX Loading: TIP4PEWBOX Loading: TIP5PBOX Loading: TP3 Loading: TP4 Loading: TP5 Loading: TPF >> HOH = OPC >> WAT = OPC >> loadAmberParams frcmod.opc Loading parameters: /home/student/Structural_bioinformatics/amber20/dat/leap/parm/frcmod.opc Reading force field modification type file (frcmod) Reading title: Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871) (UNKNOWN ATOM TYPE: EP) >> loadAmberParams frcmod.ionsjc_tip4pew Loading parameters: /home/student/Structural_bioinformatics/amber20/dat/leap/parm/frcmod.ionsjc_tip4pew Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008) >> loadAmberParams frcmod.ions234lm_126_tip4pew Loading parameters: /home/student/Structural_bioinformatics/amber20/dat/leap/parm/frcmod.ions234lm_126_tip4pew Reading force field modification type file (frcmod) Reading title: Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water model (12-6 normal usage set) >> > > source leaprc.gaff2 ----- Source: /home/student/Structural_bioinformatics/amber20/dat/leap/cmd/leaprc.gaff2 ----- Source of /home/student/Structural_bioinformatics/amber20/dat/leap/cmd/leaprc.gaff2 done >> logFile leap.log log started: Wed Mar 26 11:18:03 2025 Log file: ./leap.log >> # >> # ----- leaprc for loading the general Amber Force field. >> # This file is mostly for use with Antechamber >> # >> # load atom type hybridizations >> # >> addAtomTypes { >> { "h1" "H" "sp3" } >> { "h2" "H" "sp3" } >> { "h3" "H" "sp3" } >> { "h4" "H" "sp3" } >> { "h5" "H" "sp3" } >> { "ha" "H" "sp3" } >> { "hc" "H" "sp3" } >> { "hn" "H" "sp3" } >> { "ho" "H" "sp3" } >> { "hp" "H" "sp3" } >> { "hs" "H" "sp3" } >> { "hw" "H" "sp3" } >> { "hx" "H" "sp3" } >> { "o" "O" "sp2" } >> { "o2" "O" "sp2" } >> { "oh" "O" "sp3" } >> { "op" "O" "sp3" } >> { "oq" "O" "sp3" } >> { "os" "O" "sp3" } >> { "ow" "O" "sp3" } >> { "c" "C" "sp2" } >> { "c1" "C" "sp2" } >> { "c2" "C" "sp2" } >> { "c3" "C" "sp3" } >> { "ca" "C" "sp2" } >> { "cc" "C" "sp2" } >> { "cd" "C" "sp2" } >> { "ce" "C" "sp2" } >> { "cf" "C" "sp2" } >> { "cg" "C" "sp2" } >> { "ch" "C" "sp2" } >> { "cp" "C" "sp2" } >> { "cs" "C" "sp2" } >> { "cq" "C" "sp2" } >> { "cu" "C" "sp2" } >> { "cv" "C" "sp2" } >> { "cx" "C" "sp2" } >> { "cy" "C" "sp2" } >> { "cz" "C" "sp2" } >> { "n" "N" "sp2" } >> { "n1" "N" "sp2" } >> { "n2" "N" "sp2" } >> { "n3" "N" "sp3" } >> { "n4" "N" "sp3" } >> { "n5" "N" "sp3" } >> { "n6" "N" "sp3" } >> { "n7" "N" "sp3" } >> { "n8" "N" "sp3" } >> { "n9" "N" "sp3" } >> { "na" "N" "sp2" } >> { "nb" "N" "sp2" } >> { "nc" "N" "sp2" } >> { "nd" "N" "sp2" } >> { "ne" "N" "sp2" } >> { "nf" "N" "sp2" } >> { "nh" "N" "sp2" } >> { "ni" "N" "sp2" } >> { "nj" "N" "sp2" } >> { "nk" "N" "sp3" } >> { "nl" "N" "sp3" } >> { "nm" "N" "sp2" } >> { "nn" "N" "sp2" } >> { "no" "N" "sp2" } >> { "np" "N" "sp3" } >> { "nq" "N" "sp3" } >> { "ns" "N" "sp2" } >> { "nt" "N" "sp2" } >> { "nu" "N" "sp2" } >> { "nv" "N" "sp2" } >> { "nx" "N" "sp3" } >> { "ny" "N" "sp3" } >> { "nz" "N" "sp3" } >> { "n+" "N" "sp3" } >> { "s" "S" "sp2" } >> { "s2" "S" "sp2" } >> { "s3" "S" "sp3" } >> { "s4" "S" "sp3" } >> { "s6" "S" "sp3" } >> { "sh" "S" "sp3" } >> { "sp" "S" "sp3" } >> { "sq" "S" "sp3" } >> { "ss" "S" "sp3" } >> { "sx" "S" "sp3" } >> { "sy" "S" "sp3" } >> { "p2" "P" "sp2" } >> { "p3" "P" "sp3" } >> { "p4" "P" "sp3" } >> { "p5" "P" "sp3" } >> { "pb" "P" "sp3" } >> { "pc" "P" "sp3" } >> { "pd" "P" "sp3" } >> { "pe" "P" "sp3" } >> { "pf" "P" "sp3" } >> { "px" "P" "sp3" } >> { "py" "P" "sp3" } >> { "f" "F" "sp3" } >> { "cl" "Cl" "sp3" } >> { "br" "Br" "sp3" } >> { "i" "I" "sp3" } >> } >> # >> # Load the general force field parameter set. >> # >> gaff = loadamberparams gaff2.dat Loading parameters: /home/student/Structural_bioinformatics/amber20/dat/leap/parm/gaff2.dat Reading title: AMBER General Force Field for organic molecules (Version 2.11, May 2016) > > loadamberparams dar.frcmod Loading parameters: ./dar.frcmod Reading force field modification type file (frcmod) Reading title: Remark line goes here > loadoff dar.lib Loading library: ./dar.lib Loading: DAR > protein = loadpdb mut.pdb Loading PDB file: ./mut.pdb Matching PDB residue names to LEaP variables. Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO. Mapped residue PHE, term: Terminal/last, seq. number: 98 to: CPHE. Mapped residue PRO, term: Terminal/beginning, seq. number: 99 to: NPRO. Mapped residue PHE, term: Terminal/last, seq. number: 197 to: CPHE. total atoms in file: 3131 > ligand = loadpdb darunavir_clean.pdb Loading PDB file: ./darunavir_clean.pdb (starting new molecule for chain B) Matching PDB residue names to LEaP variables. total atoms in file: 76 Leap added 74 missing atoms according to residue templates: 74 H / lone pairs > waters = loadpdb waters_clean.pdb Loading PDB file: ./waters_clean.pdb (starting new molecule for chain B) Matching PDB residue names to LEaP variables. Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC Starting new chain with OPC total atoms in file: 94 Leap added 282 missing atoms according to residue templates: 282 H / lone pairs > system = combine { protein ligand waters } Sequence: default_name Sequence: default_name Sequence: default_name > charge system Total unperturbed charge: 6.996004 Total perturbed charge: 6.996004 > solvateoct system OPCBOX 8 Scaling up box by a factor of 1.170057 to meet diagonal cut criterion Solute vdw bounding box: 38.839 41.820 64.035 Total bounding box for atom centers: 82.756 82.756 82.756 (box expansion for 'iso' is 96.5%) Solvent unit box: 18.865 18.478 19.006 The number of boxes: x= 5 y= 5 z= 5 Volume: 293772.279 A^3 (oct) Total mass 157195.408 amu, Density 0.889 g/cc Added 7374 residues. > addions K+ 16 addIons unit ion1 #ion1 [ion2 #ion2] UNIT _unit_ UNIT _ion1_ NUMBER _#ion1_ UNIT _ion2_ NUMBER _#ion2_ Adds counterions in a shell around _unit_ using a Coulombic potential on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise, the specified numbers of _ion1_ [_ion2_] are added [in alternating order]. If solvent is present, it is ignored in the charge and steric calculations, and if an ion has a steric conflict with a solvent molecule, the ion is moved to the center of said molecule, and the latter is deleted. (To avoid this behavior, either solvate _after_ addIons, or use addIons2.) Ions must be monoatomic. Note that the one-at-a-time procedure is not guaranteed to globally minimize the electrostatic energy. When neutralizing regular-backbone nucleic acids, the first cations will generally be added between phosphates, leaving the final two ions to be placed somewhere around the middle of the molecule. The default grid resolution is 1 Angstrom, extending from an inner radius of (max ion size + max solute atom size) to an outer radius 4 Angstroms beyond. A distance-dependent dielectric is used for speed. > addions system K+ 16 Adding 16 counter ions to "system" using 1A grid Total solute charge: 7.00 Max atom radius: 1.98 Grid extends from solute vdw + 4.09 to 10.07 Box: enclosing: -32.09 -35.52 -29.62 36.51 36.70 28.82 sized: 95.91 92.48 98.38 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 Volume = 2.65% of box, grid points 55483 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed K+ in system at (-19.73, 1.15, 12.73). (Replacing solvent molecule) Placed K+ in system at (9.13, -20.80, -0.81). (Replacing solvent molecule) Placed K+ in system at (6.00, 7.89, -17.57). (Replacing solvent molecule) Placed K+ in system at (-5.58, 14.15, 17.05). (Replacing solvent molecule) Placed K+ in system at (9.37, -2.94, -24.01). (Replacing solvent molecule) Placed K+ in system at (-8.20, 19.17, -10.38). (Replacing solvent molecule) Placed K+ in system at (-0.65, -14.34, 18.00). (Replacing solvent molecule) Placed K+ in system at (6.22, 16.75, 16.10). (Replacing solvent molecule) Placed K+ in system at (-22.38, -4.76, 5.08). (Replacing solvent molecule) Placed K+ in system at (-3.22, -33.97, -0.40). (Replacing solvent molecule) Placed K+ in system at (14.99, 29.36, -14.79). (Replacing solvent molecule) Placed K+ in system at (12.54, -9.76, -15.96). (Replacing solvent molecule) Placed K+ in system at (34.01, 24.55, 5.47). (Replacing solvent molecule) Placed K+ in system at (-28.71, -28.08, -12.14). (Replacing solvent molecule) Placed K+ in system at (-24.95, 14.76, 13.77). (Replacing solvent molecule) Placed K+ in system at (-5.97, -32.13, 17.32). Done adding ions. > addions system Cl- 23 Adding 23 counter ions to "system" using 1A grid Total solute charge: 23.00 Max atom radius: 1.98 Grid extends from solute vdw + 7.96 to 13.94 Box: enclosing: -42.66 -47.91 -37.96 47.96 43.30 32.70 sized: 85.34 80.09 90.04 edge: 128.00 Resolution: 1.00 Angstrom. Tree depth: 7 Volume = 4.21% of box, grid points 88368 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges (Replacing solvent molecule) Placed Cl- in system at (17.94, -1.27, -18.72). (Replacing solvent molecule) Placed Cl- in system at (-26.31, 7.45, 8.56). (Replacing solvent molecule) Placed Cl- in system at (0.25, -33.05, 7.42). (Replacing solvent molecule) Placed Cl- in system at (-9.74, 8.35, -18.38). (Replacing solvent molecule) Placed Cl- in system at (15.37, 0.16, 13.23). (Replacing solvent molecule) Placed Cl- in system at (-26.20, -23.65, -4.34). (Replacing solvent molecule) Placed Cl- in system at (25.96, 28.36, 3.08). (Replacing solvent molecule) Placed Cl- in system at (8.59, -14.33, -25.18). (Replacing solvent molecule) Placed Cl- in system at (-3.36, -5.93, 23.66). (Replacing solvent molecule) Placed Cl- in system at (-14.78, 17.91, -2.91). (Replacing solvent molecule) Placed Cl- in system at (-14.46, -27.34, 18.06). (Replacing solvent molecule) Placed Cl- in system at (32.90, 14.68, 3.75). (Replacing solvent molecule) Placed Cl- in system at (-19.30, -18.16, -20.91). (Replacing solvent molecule) Placed Cl- in system at (0.94, 21.14, 19.58). (Replacing solvent molecule) Placed Cl- in system at (-26.93, -5.56, 15.52). (Replacing solvent molecule) Placed Cl- in system at (-3.26, -32.47, -8.98). (Replacing solvent molecule) Placed Cl- in system at (7.08, 30.94, -12.44). (Replacing solvent molecule) Placed Cl- in system at (7.13, 5.09, -27.67). (Replacing solvent molecule) Placed Cl- in system at (-0.84, -24.67, 22.31). (Replacing solvent molecule) Placed Cl- in system at (-13.76, 16.25, 16.45). (Replacing solvent molecule) Placed Cl- in system at (33.68, 0.92, -4.77). (Replacing solvent molecule) Placed Cl- in system at (-19.19, -30.29, -14.24). (Replacing solvent molecule) Placed Cl- in system at (23.29, 22.80, -12.69). Done adding ions. > charge system Total unperturbed charge: -0.003996 Total perturbed charge: -0.003996 > check system Checking 'system'.... Warning: Close contact of 1.327919 angstroms between .R.A and .R.A Warning: Close contact of 1.310745 angstroms between .R.A and .R.A

Warning: Close contact of 1.428073 angstroms between .R.A and .R.A

Warning: Close contact of 1.455057 angstroms between .R.A and .R.A

Warning: Close contact of 1.243060 angstroms between .R.A and .R.A

Warning: Close contact of 1.253876 angstroms between .R.A and .R.A

Warning: Close contact of 1.461604 angstroms between .R.A and .R.A

Warning: Close contact of 1.199687 angstroms between .R.A and .R.A

Warning: Close contact of 1.466291 angstroms between .R.A and .R.A

Checking parameters for unit 'system'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 22296 Unit is OK. > saveamberparm system mut_protease.prmtop mut_protease.inpcrd Checking Unit. Note: Ignoring the warnings from Unit Checking. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 604 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 CPHE 2 DAR 2 NPRO 2 WAT 94 ) (no restraints) > savepdb system mut_protease.pdb Writing pdb file: mut_protease.pdb printing CRYST1 record to PDB file with box info Warning: Converting N-terminal residue name to PDB format: NPRO -> PRO Warning: Converting C-terminal residue name to PDB format: CPHE -> PHE Warning: Converting N-terminal residue name to PDB format: NPRO -> PRO Warning: Converting C-terminal residue name to PDB format: CPHE -> PHE > quit Quit Exiting LEaP: Errors = 0; Warnings = 13; Notes = 1.