log started: Thu Jan 5 12:23:24 2017 Log file: ./leap.log > # > # ----- leaprc for loading the ff14SB 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" } > { "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. > # > parm10 = loadamberparams parm10.dat Loading parameters: /usr/local/src/amber16/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) > frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /usr/local/src/amber16/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters > # > # Load main chain and terminating amino acid libraries > # > loadOff amino12.lib Loading library: /usr/local/src/amber16/dat/leap/lib/amino12.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: /usr/local/src/amber16/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: /usr/local/src/amber16/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 > loadoff solvents.lib Loading library: /usr/local/src/amber16/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC 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 > loadoff atomic_ions.lib Loading library: /usr/local/src/amber16/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 > loadamberparams frcmod.tip4pfb Loading parameters: /usr/local/src/amber16/dat/leap/parm/frcmod.tip4pfb Reading force field modification type file (frcmod) Reading title: TIP4P-FB Water Model (Wang, Martinez, Pande, J. Phys. Chem. Lett., 5:1885, 2014) (UNKNOWN ATOM TYPE: EP) > list ACE AG AL ALA ARG ASH ASN ASP Ag BA BR Be CA CALA CARG CASN CASP CCYS CCYX CD CE CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CHYP CILE CL CLEU CLYS CMET CO CPHE CPRO CR CS CSER CTHR CTRP CTYR CU CU1 CVAL CYM CYS CYX Ce Cl- Cr DC4 Dy EU EU3 Er F FB3 FB3BOX FB4 FB4BOX FE FE2 GD3 GLH GLN GLU GLY H3O+ HE+ HG HID HIE HIP HIS HYP HZ+ Hf ILE IN IOD K K+ LA LEU LI LU LYN LYS MEOHBOX MET MG MN NA NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NH4 NHE NHID NHIE NHIP NHIS NI NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ Nd OPC OPCBOX PB PD PHE PL3 POL3BOX PR PRO PT Pu QSPCFWBOX RB Ra SER SM SPC SPCBOX SPCFWBOX SPF SPG SR Sm Sn T4E TB THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOXTIP5PBOX TL TP3 TP4 TP5 TPF TRP TYR Th Tl Tm U4+ V2+ VAL Y YB2 ZN Zr frcmod14SBparm10 > test = sequence {ACE LYS NME} Sequence: ACE Sequence: LYS Joining ACE - LYS Sequence: NME Joining LYS - NME > solvateoct test FB4BOX 8.0 Scaling up box by a factor of 1.254194 to meet diagonal cut criterion Solute vdw bounding box: 13.136 9.519 5.710 Total bounding box for atom centers: 33.203 33.203 33.203 (box expansion for 'iso' is 44.6%) Solvent unit box: 18.794 18.794 18.794 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.397000, 9.397000, 9.397000 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.397000, 9.397000, -9.397000 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.397000, -9.397000, 9.397000 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.397000, -9.397000, -9.397000 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.397000, 9.397000, 9.397000 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.397000, 9.397000, -9.397000 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.397000, -9.397000, 9.397000 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.397000, -9.397000, -9.397000 Volume: 20006.004 A^3 (oct) Total mass 9498.536 amu, Density 0.788 g/cc Added 516 residues. > addions test Na+ 3 Using default radius 1.50 for ion Na+ Adding 3 counter ions to "test" using 1A grid Total solute charge: 1.00 Max atom radius: 1.91 Grid extends from solute vdw + 1.50 to 7.41 Box: enclosing: -9.39 -10.92 -13.07 12.43 9.08 10.54 sized: 22.61 21.08 18.93 edge: 32.00 Resolution: 1.00 Angstrom. Tree depth: 5 grid build: 0 sec Volume = 12.98% of box, grid points 4254 Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 0 sec (Replacing solvent molecule) Placed Na+ in test at (0.60, -3.97, -5.69). (Replacing solvent molecule) Placed Na+ in test at (-4.75, 3.43, 1.35). (Replacing solvent molecule) Placed Na+ in test at (2.79, 7.21, -8.90). Done adding ions. > charge test Total unperturbed charge: 4.000000 Total perturbed charge: 4.000000 > check test Checking 'test'.... WARNING: The unperturbed charge of the unit: 4.000000 is not zero. Warning: Close contact of 1.246713 angstroms between .R.A and .R.A Checking parameters for unit 'test'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 1541 Unit is OK. > saveamberparm test test.prmtop test.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 4.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. For atom: .R.A Could not find vdW (or other) parameters for type: Na+ For atom: .R.A Could not find vdW (or other) parameters for type: Na+ For atom: .R.A Could not find vdW (or other) parameters for type: Na+ Parameter file was not saved. > savepdb test test.pdb Writing pdb file: test.pdb printing CRYST1 record to PDB file with box info > quit Quit log started: Thu Jan 5 12:33:39 2017 Log file: ./leap.log > # > # ----- leaprc for loading the ff14SB 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" } > { "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. > # > parm10 = loadamberparams parm10.dat Loading parameters: /usr/local/src/amber16/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA (UNKNOWN ATOM TYPE: Zn) (UNKNOWN ATOM TYPE: EP) > frcmod14SB = loadamberparams frcmod.ff14SB Loading parameters: /usr/local/src/amber16/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters > # > # Load main chain and terminating amino acid libraries > # > loadOff amino12.lib Loading library: /usr/local/src/amber16/dat/leap/lib/amino12.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: /usr/local/src/amber16/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: /usr/local/src/amber16/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 > loadoff solvents.lib Loading library: /usr/local/src/amber16/dat/leap/lib/solvents.lib Loading: CHCL3BOX Loading: DC4 Loading: FB3 Loading: FB3BOX Loading: FB4 Loading: FB4BOX Loading: MEOHBOX Loading: NMABOX Loading: OPC 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 > loadoff atomic_ions.lib Loading library: /usr/local/src/amber16/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 > loadamberparams frcmod.tip4pfb Loading parameters: /usr/local/src/amber16/dat/leap/parm/frcmod.tip4pfb Reading force field modification type file (frcmod) Reading title: TIP4P-FB Water Model (Wang, Martinez, Pande, J. Phys. Chem. Lett., 5:1885, 2014) (UNKNOWN ATOM TYPE: EP) > list ACE AG AL ALA ARG ASH ASN ASP Ag BA BR Be CA CALA CARG CASN CASP CCYS CCYX CD CE CGLN CGLU CGLY CHCL3BOX CHID CHIE CHIP CHIS CHYP CILE CL CLEU CLYS CMET CO CPHE CPRO CR CS CSER CTHR CTRP CTYR CU CU1 CVAL CYM CYS CYX Ce Cl- Cr DC4 Dy EU EU3 Er F FB3 FB3BOX FB4 FB4BOX FE FE2 GD3 GLH GLN GLU GLY H3O+ HE+ HG HID HIE HIP HIS HYP HZ+ Hf ILE IN IOD K K+ LA LEU LI LU LYN LYS MEOHBOX MET MG MN NA NALA NARG NASN NASP NCYS NCYX NGLN NGLU NGLY NH4 NHE NHID NHIE NHIP NHIS NI NILE NLEU NLYS NMABOX NME NMET NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+ Nd OPC OPCBOX PB PD PHE PL3 POL3BOX PR PRO PT Pu QSPCFWBOX RB Ra SER SM SPC SPCBOX SPCFWBOX SPF SPG SR Sm Sn T4E TB THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOXTIP5PBOX TL TP3 TP4 TP5 TPF TRP TYR Th Tl Tm U4+ V2+ VAL Y YB2 ZN Zr frcmod14SBparm10 > test = sequence {ACE LYS NME} Sequence: ACE Sequence: LYS Joining ACE - LYS Sequence: NME Joining LYS - NME > charge test Total unperturbed charge: 1.000000 Total perturbed charge: 1.000000 > solvateoct test FB4BOX 8.0 Scaling up box by a factor of 1.254194 to meet diagonal cut criterion Solute vdw bounding box: 13.136 9.519 5.710 Total bounding box for atom centers: 33.203 33.203 33.203 (box expansion for 'iso' is 44.6%) Solvent unit box: 18.794 18.794 18.794 The number of boxes: x= 2 y= 2 z= 2 Adding box at: x=0 y=0 z=0 Center of solvent box is: 9.397000, 9.397000, 9.397000 Adding box at: x=0 y=0 z=1 Center of solvent box is: 9.397000, 9.397000, -9.397000 Adding box at: x=0 y=1 z=0 Center of solvent box is: 9.397000, -9.397000, 9.397000 Adding box at: x=0 y=1 z=1 Center of solvent box is: 9.397000, -9.397000, -9.397000 Adding box at: x=1 y=0 z=0 Center of solvent box is: -9.397000, 9.397000, 9.397000 Adding box at: x=1 y=0 z=1 Center of solvent box is: -9.397000, 9.397000, -9.397000 Adding box at: x=1 y=1 z=0 Center of solvent box is: -9.397000, -9.397000, 9.397000 Adding box at: x=1 y=1 z=1 Center of solvent box is: -9.397000, -9.397000, -9.397000 Volume: 20006.004 A^3 (oct) Total mass 9498.536 amu, Density 0.788 g/cc Added 516 residues. > addions2 test Na+ 2 Using default radius 1.50 for ion Na+ Adding 2 counter ions to "test" using 1A grid Total solute charge: 1.00 Max atom radius: 1.91 Grid extends from solute vdw + 1.50 to 7.41 Box: enclosing: -21.60 -23.49 -23.76 21.91 23.63 24.37 sized: 42.40 40.51 40.24 edge: 64.00 Resolution: 1.00 Angstrom. Tree depth: 6 grid build: 0 sec Volume = 10.30% of box, grid points 27010 Calculating grid charges charges: 1 sec Placed Na+ in test at (-4.60, -11.49, 9.24). Placed Na+ in test at (-15.60, -3.49, 4.24). Done adding ions. > charge test Total unperturbed charge: 3.000000 Total perturbed charge: 3.000000 > savepdb test test.pdb Writing pdb file: test.pdb printing CRYST1 record to PDB file with box info > saveamberparm test test.prmtop test.inpcrd Checking Unit. WARNING: The unperturbed charge of the unit: 3.000000 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. For atom: .R.A Could not find vdW (or other) parameters for type: Na+ For atom: .R.A Could not find vdW (or other) parameters for type: Na+ Parameter file was not saved. > quit Quit