On Wed, Jun 28, 2017, Rana Rehan Khalid wrote:
>
> i used antechamber for my heme fe--o2 ligand it show this error and mol2
> not formed for heme-fe----O2. i also sending you the leap.log kindly tell
> me where i am wrong
Antechamber doesn't work for transition metal systems. You will need to learn
to use MCPB or a similar program.
My suggestion: start with a deoxy heme (no ligand): make sure that you can
create and run short MD runs for such a system. Then, adding in the ligand
is not hard, assuming you understand how Amber handles these systems. The
ligand can be created by using antechamber (or, much better, taken from the
literature), and you can use a text editor to create a frcmod file that has
the needed parameters to link the ligand to the Fe-heme group.
...good luck...dac
>
> Running: /home/rehan/Downloads/amber16/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> For atom[26]:O01, the best APS is not zero, bonds involved by this atom are
> frozen
>
> For atom[45]:Fe, the best APS is not zero, bonds involved by this atom are
> frozen
>
> The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8 (aromatic
> double)Error: cannot run "/home/rehan/Downloads/amber16/bin/bondtype -j
> full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
> log started: Wed Jun 28 17:51:00 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: /home/rehan/Downloads/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: /home/rehan/Downloads/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: /home/rehan/Downloads/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: /home/rehan/Downloads/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: /home/rehan/Downloads/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
> >
> > source leaprc.gaff
> ----- Source: /home/rehan/Downloads/amber16/dat/leap/cmd/leaprc.gaff
> ----- Source of /home/rehan/Downloads/amber16/dat/leap/cmd/leaprc.gaff done
> >> logFile leap.log
> log started: Wed Jun 28 17:51:25 2017
>
> 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" }
> >> { "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" }
> >> { "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" }
> >> { "na" "N" "sp2" }
> >> { "nb" "N" "sp2" }
> >> { "nc" "N" "sp2" }
> >> { "nd" "N" "sp2" }
> >> { "ne" "N" "sp2" }
> >> { "nf" "N" "sp2" }
> >> { "nh" "N" "sp2" }
> >> { "no" "N" "sp2" }
> >> { "s" "S" "sp2" }
> >> { "s2" "S" "sp2" }
> >> { "s3" "S" "sp3" }
> >> { "s4" "S" "sp3" }
> >> { "s6" "S" "sp3" }
> >> { "sh" "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 gaff.dat
> Loading parameters: /home/rehan/Downloads/amber16/dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
> >
> > hem = loadmol2 new.mol2
> Loading Mol2 file: ./new.mol2
> Reading MOLECULE named hem_h.pdb
> > list
> ACE ALA ARG ASH ASN ASP CALA CARG
> CASN CASP CCYS CCYX CGLN CGLU CGLY CHID
> CHIE CHIP CHIS CHYP CILE CLEU CLYS CMET
> CPHE CPRO CSER CTHR CTRP CTYR CVAL CYM
> CYS CYX GLH GLN GLU GLY HID HIE
> HIP HIS HYP ILE LEU LYN LYS MET
> NALA NARG NASN NASP NCYS NCYX NGLN NGLU
> NGLY NHE NHID NHIE NHIP NHIS NILE NLEU
> NLYS NME NMET NPHE NPRO NSER NTHR NTRP
> NTYR NVAL PHE PRO SER THR TRP TYR
> VAL frcmod14SBgaff hem parm10
> > check hem
> Checking 'hem'....
> Warning: Close contact of 1.450054 angstroms between .R<HEM 1>.A<O01 26> and .R<HEM 1>.A<FE 45>
> Checking parameters for unit 'hem'.
> Checking for bond parameters.
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - C.3
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.2 - C.ar
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.3 - C.ar
> Could not find bond parameter for: C.3 - C.3
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: C.2 - O.co2
> Could not find bond parameter for: C.2 - O.co2
> Could not find bond parameter for: C.2 - O.co2
> Could not find bond parameter for: C.2 - O.co2
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - H
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - H
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - H
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - H
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - C.ar
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - C.ar
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.ar - C.2
> Could not find bond parameter for: C.ar - C.2
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - N.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: O.3 - O.3
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.2 - C.ar
> Could not find bond parameter for: C.2 - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - N.ar
> Checking for angle parameters.
> Could not find angle parameter: C.3 - C.2 - C.ar
> Could not find angle parameter: C.3 - C.2 - C.2
> Could not find angle parameter: C.3 - C.3 - C.2
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.2 - C.2 - C.2
> Could not find angle parameter: C.2 - C.2 - C.ar
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.2 - C.ar - C.ar
> Could not find angle parameter: C.2 - C.ar - C.ar
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.3 - C.2
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.2
> Could not find angle parameter: N.ar - C.ar - C.2
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: C.3 - C.3 - C.2
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.2 - O.co2
> Could not find angle parameter: C.3 - C.2 - O.co2
> Could not find angle parameter: C.2 - C.2 - C.2
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.2 - C.2 - C.ar
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.3 - C.3 - C.ar
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.2 - O.co2
> Could not find angle parameter: C.3 - C.2 - O.co2
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.2
> Could not find angle parameter: N.ar - C.ar - C.2
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.2
> Could not find angle parameter: C.ar - C.ar - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - N.ar
> Could not find angle parameter: C.ar - C.ar - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - N.ar
> Could not find angle parameter: C.3 - C.2 - C.2
> Could not find angle parameter: C.3 - C.2 - C.ar
> Could not find angle parameter: C.3 - C.2 - C.ar
> Could not find angle parameter: C.3 - C.2 - C.2
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - N.ar - C.ar
> Could not find angle parameter: C.ar - C.2 - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - N.ar - C.ar
> Could not find angle parameter: C.ar - C.2 - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - N.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - N.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: O.co2 - C.2 - O.co2
> Could not find angle parameter: O.co2 - C.2 - O.co2
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.2 - C.ar
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.2 - C.ar
> Could not find angle parameter: C.ar - C.ar - N.ar
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.ar - C.2 - H
> Could not find angle parameter: C.ar - C.ar - N.ar
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.2 - H
> Could not find angle parameter: H - C.2 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> There are missing parameters.
> check: Warnings: 1
> Unit is OK.
> > loadamberparams hem.frcmod
> Loading parameters: ./hem.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> Force field modifcations for all-atom heme /parametros Dario
> (UNKNOWN ATOM TYPE: FE)
> (UNKNOWN ATOM TYPE: FO)
> (UNKNOWN ATOM TYPE: LO)
> (UNKNOWN ATOM TYPE: LC)
> > check hem
> Checking 'hem'....
> Warning: Close contact of 1.450054 angstroms between .R<HEM 1>.A<O01 26> and .R<HEM 1>.A<FE 45>
> Checking parameters for unit 'hem'.
> Checking for bond parameters.
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - C.3
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.2 - C.ar
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.3 - C.ar
> Could not find bond parameter for: C.3 - C.3
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: C.2 - O.co2
> Could not find bond parameter for: C.2 - O.co2
> Could not find bond parameter for: C.2 - O.co2
> Could not find bond parameter for: C.2 - O.co2
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - H
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - H
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - H
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - H
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - C.ar
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - C.ar
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.ar - C.2
> Could not find bond parameter for: C.ar - C.2
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - N.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: O.3 - O.3
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.2 - C.ar
> Could not find bond parameter for: C.2 - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - N.ar
> Checking for angle parameters.
> Could not find angle parameter: C.3 - C.2 - C.ar
> Could not find angle parameter: C.3 - C.2 - C.2
> Could not find angle parameter: C.3 - C.3 - C.2
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.2 - C.2 - C.2
> Could not find angle parameter: C.2 - C.2 - C.ar
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.2 - C.ar - C.ar
> Could not find angle parameter: C.2 - C.ar - C.ar
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.3 - C.2
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.2
> Could not find angle parameter: N.ar - C.ar - C.2
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: C.3 - C.3 - C.2
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.2 - O.co2
> Could not find angle parameter: C.3 - C.2 - O.co2
> Could not find angle parameter: C.2 - C.2 - C.2
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.2 - C.2 - C.ar
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.3 - C.3 - C.ar
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.2 - O.co2
> Could not find angle parameter: C.3 - C.2 - O.co2
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.2
> Could not find angle parameter: N.ar - C.ar - C.2
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.2
> Could not find angle parameter: C.ar - C.ar - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - N.ar
> Could not find angle parameter: C.ar - C.ar - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - N.ar
> Could not find angle parameter: C.3 - C.2 - C.2
> Could not find angle parameter: C.3 - C.2 - C.ar
> Could not find angle parameter: C.3 - C.2 - C.ar
> Could not find angle parameter: C.3 - C.2 - C.2
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - N.ar - C.ar
> Could not find angle parameter: C.ar - C.2 - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - N.ar - C.ar
> Could not find angle parameter: C.ar - C.2 - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - N.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - N.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: O.co2 - C.2 - O.co2
> Could not find angle parameter: O.co2 - C.2 - O.co2
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.2 - C.ar
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.2 - C.ar
> Could not find angle parameter: C.ar - C.ar - N.ar
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.ar - C.2 - H
> Could not find angle parameter: C.ar - C.ar - N.ar
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.2 - H
> Could not find angle parameter: H - C.2 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> There are missing parameters.
> check: Warnings: 1
> Unit is OK.
> > loadamberparams hem.frcmod
> Loading parameters: ./hem.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> Force field modifcations for all-atom heme /parametros Dario
> (UNKNOWN ATOM TYPE: FE)
> (UNKNOWN ATOM TYPE: FO)
> (UNKNOWN ATOM TYPE: LO)
> (UNKNOWN ATOM TYPE: LC)
> > check hem
> Checking 'hem'....
> Warning: Close contact of 1.450054 angstroms between .R<HEM 1>.A<O01 26> and .R<HEM 1>.A<FE 45>
> Checking parameters for unit 'hem'.
> Checking for bond parameters.
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - C.3
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.2 - C.ar
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.3 - C.ar
> Could not find bond parameter for: C.3 - C.3
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.2 - H
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: C.2 - O.co2
> Could not find bond parameter for: C.2 - O.co2
> Could not find bond parameter for: C.2 - O.co2
> Could not find bond parameter for: C.2 - O.co2
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: N.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - H
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - H
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - H
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - H
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - C.2
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - C.ar
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - C.ar
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.3 - H
> Could not find bond parameter for: C.ar - C.2
> Could not find bond parameter for: C.ar - C.2
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - N.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: O.3 - O.3
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.2 - C.2
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.2 - C.ar
> Could not find bond parameter for: C.2 - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - C.ar
> Could not find bond parameter for: C.ar - N.ar
> Checking for angle parameters.
> Could not find angle parameter: C.3 - C.2 - C.ar
> Could not find angle parameter: C.3 - C.2 - C.2
> Could not find angle parameter: C.3 - C.3 - C.2
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.2 - C.2 - C.2
> Could not find angle parameter: C.2 - C.2 - C.ar
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.2 - C.ar - C.ar
> Could not find angle parameter: C.2 - C.ar - C.ar
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.3 - C.2
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.2
> Could not find angle parameter: N.ar - C.ar - C.2
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: C.3 - C.3 - C.2
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.2 - O.co2
> Could not find angle parameter: C.3 - C.2 - O.co2
> Could not find angle parameter: C.2 - C.2 - C.2
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.2 - C.2 - C.ar
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.3 - C.3 - C.ar
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.3 - H
> Could not find angle parameter: C.3 - C.2 - O.co2
> Could not find angle parameter: C.3 - C.2 - O.co2
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.2
> Could not find angle parameter: N.ar - C.ar - C.2
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: N.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.2
> Could not find angle parameter: C.ar - C.ar - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - N.ar
> Could not find angle parameter: C.ar - C.ar - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - N.ar
> Could not find angle parameter: C.3 - C.2 - C.2
> Could not find angle parameter: C.3 - C.2 - C.ar
> Could not find angle parameter: C.3 - C.2 - C.ar
> Could not find angle parameter: C.3 - C.2 - C.2
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.3 - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - N.ar - C.ar
> Could not find angle parameter: C.ar - C.2 - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - N.ar - C.ar
> Could not find angle parameter: C.ar - C.2 - C.2
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - N.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - N.ar - C.ar
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: O.co2 - C.2 - O.co2
> Could not find angle parameter: O.co2 - C.2 - O.co2
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.2 - C.ar
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.2 - C.ar
> Could not find angle parameter: C.ar - C.ar - N.ar
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.ar - C.ar
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.3 - H
> Could not find angle parameter: C.2 - C.2 - H
> Could not find angle parameter: C.ar - C.2 - H
> Could not find angle parameter: C.ar - C.ar - N.ar
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.3 - H
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: C.ar - C.ar - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.2 - H
> Could not find angle parameter: H - C.2 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> Could not find angle parameter: H - C.3 - H
> There are missing parameters.
> check: Warnings: 1
> Unit is OK.
> > saveoff HEM hem.lib
> saveOff: Argument #1 is type String must be of type: [unit parameter_set list]
> usage: saveOff <object> <filename>
> > saveoff hem hem.lib
> Creating hem.lib
> Saving hem.
> Building topology.
> Building atom parameters.
> > loadoff hem.lib
> Loading library: ./hem.lib
> Loading: hem
> > complex = loadpdb 1FKO_trunc_sus.pdb
> Could not open file 1FKO_trunc_sus.pdb: not found
> > complex = loadpdb hnoxo.pdb
> Loading PDB file: ./hnoxo.pdb
> Enter zPdbReadScan from call depth 0.
> Exit zPdbReadScan from call depth 0.
> Matching PDB residue names to LEaP variables.
> Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET.
> (Residue 1: TYR, Nonterminal, was not found in name map.)
> (Residue 2: GLY, Nonterminal, was not found in name map.)
> (Residue 3: PHE, Nonterminal, was not found in name map.)
> (Residue 4: VAL, Nonterminal, was not found in name map.)
> (Residue 5: ASN, Nonterminal, was not found in name map.)
> (Residue 6: HIS, Nonterminal, was not found in name map.)
> (Residue 7: ALA, Nonterminal, was not found in name map.)
> (Residue 8: LEU, Nonterminal, was not found in name map.)
> (Residue 9: GLU, Nonterminal, was not found in name map.)
> (Residue 10: LEU, Nonterminal, was not found in name map.)
> (Residue 11: LEU, Nonterminal, was not found in name map.)
> (Residue 12: VAL, Nonterminal, was not found in name map.)
> (Residue 13: ILE, Nonterminal, was not found in name map.)
> (Residue 14: ARG, Nonterminal, was not found in name map.)
> (Residue 15: ASN, Nonterminal, was not found in name map.)
> (Residue 16: TYR, Nonterminal, was not found in name map.)
> (Residue 17: GLY, Nonterminal, was not found in name map.)
> (Residue 18: PRO, Nonterminal, was not found in name map.)
> (Residue 19: GLU, Nonterminal, was not found in name map.)
> (Residue 20: VAL, Nonterminal, was not found in name map.)
> (Residue 21: TRP, Nonterminal, was not found in name map.)
> (Residue 22: GLU, Nonterminal, was not found in name map.)
> (Residue 23: ASP, Nonterminal, was not found in name map.)
> (Residue 24: ILE, Nonterminal, was not found in name map.)
> (Residue 25: LYS, Nonterminal, was not found in name map.)
> (Residue 26: LYS, Nonterminal, was not found in name map.)
> (Residue 27: GLU, Nonterminal, was not found in name map.)
> (Residue 28: ALA, Nonterminal, was not found in name map.)
> (Residue 29: GLN, Nonterminal, was not found in name map.)
> (Residue 30: LEU, Nonterminal, was not found in name map.)
> (Residue 31: ASP, Nonterminal, was not found in name map.)
> (Residue 32: GLU, Nonterminal, was not found in name map.)
> (Residue 33: GLU, Nonterminal, was not found in name map.)
> (Residue 34: GLY, Nonterminal, was not found in name map.)
> (Residue 35: GLN, Nonterminal, was not found in name map.)
> (Residue 36: PHE, Nonterminal, was not found in name map.)
> (Residue 37: LEU, Nonterminal, was not found in name map.)
> (Residue 38: VAL, Nonterminal, was not found in name map.)
> (Residue 39: ARG, Nonterminal, was not found in name map.)
> (Residue 40: ILE, Nonterminal, was not found in name map.)
> (Residue 41: ILE, Nonterminal, was not found in name map.)
> (Residue 42: TYR, Nonterminal, was not found in name map.)
> (Residue 43: ASP, Nonterminal, was not found in name map.)
> (Residue 44: ASP, Nonterminal, was not found in name map.)
> (Residue 45: SER, Nonterminal, was not found in name map.)
> (Residue 46: LYS, Nonterminal, was not found in name map.)
> (Residue 47: THR, Nonterminal, was not found in name map.)
> (Residue 48: TYR, Nonterminal, was not found in name map.)
> (Residue 49: ASP, Nonterminal, was not found in name map.)
> (Residue 50: LEU, Nonterminal, was not found in name map.)
> (Residue 51: VAL, Nonterminal, was not found in name map.)
> (Residue 52: ALA, Nonterminal, was not found in name map.)
> (Residue 53: ALA, Nonterminal, was not found in name map.)
> (Residue 54: ALA, Nonterminal, was not found in name map.)
> (Residue 55: SER, Nonterminal, was not found in name map.)
> (Residue 56: LYS, Nonterminal, was not found in name map.)
> (Residue 57: VAL, Nonterminal, was not found in name map.)
> (Residue 58: LEU, Nonterminal, was not found in name map.)
> (Residue 59: ASN, Nonterminal, was not found in name map.)
> (Residue 60: LEU, Nonterminal, was not found in name map.)
> (Residue 61: ASN, Nonterminal, was not found in name map.)
> (Residue 62: ALA, Nonterminal, was not found in name map.)
> (Residue 63: GLY, Nonterminal, was not found in name map.)
> (Residue 64: GLU, Nonterminal, was not found in name map.)
> (Residue 65: ILE, Nonterminal, was not found in name map.)
> (Residue 66: LEU, Nonterminal, was not found in name map.)
> (Residue 67: GLN, Nonterminal, was not found in name map.)
> (Residue 68: MET, Nonterminal, was not found in name map.)
> (Residue 69: PHE, Nonterminal, was not found in name map.)
> (Residue 70: GLY, Nonterminal, was not found in name map.)
> (Residue 71: LYS, Nonterminal, was not found in name map.)
> (Residue 72: MET, Nonterminal, was not found in name map.)
> (Residue 73: PHE, Nonterminal, was not found in name map.)
> (Residue 74: PHE, Nonterminal, was not found in name map.)
> (Residue 75: VAL, Nonterminal, was not found in name map.)
> (Residue 76: PHE, Nonterminal, was not found in name map.)
> (Residue 77: CYS, Nonterminal, was not found in name map.)
> (Residue 78: GLN, Nonterminal, was not found in name map.)
> (Residue 79: GLU, Nonterminal, was not found in name map.)
> (Residue 80: SER, Nonterminal, was not found in name map.)
> (Residue 81: GLY, Nonterminal, was not found in name map.)
> (Residue 82: TYR, Nonterminal, was not found in name map.)
> (Residue 83: ASP, Nonterminal, was not found in name map.)
> (Residue 84: THR, Nonterminal, was not found in name map.)
> (Residue 85: ILE, Nonterminal, was not found in name map.)
> (Residue 86: LEU, Nonterminal, was not found in name map.)
> (Residue 87: ARG, Nonterminal, was not found in name map.)
> (Residue 88: VAL, Nonterminal, was not found in name map.)
> (Residue 89: LEU, Nonterminal, was not found in name map.)
> (Residue 90: GLY, Nonterminal, was not found in name map.)
> (Residue 91: SER, Nonterminal, was not found in name map.)
> (Residue 92: ASN, Nonterminal, was not found in name map.)
> (Residue 93: VAL, Nonterminal, was not found in name map.)
> (Residue 94: ARG, Nonterminal, was not found in name map.)
> (Residue 95: GLU, Nonterminal, was not found in name map.)
> (Residue 96: PHE, Nonterminal, was not found in name map.)
> (Residue 97: LEU, Nonterminal, was not found in name map.)
> (Residue 98: GLN, Nonterminal, was not found in name map.)
> (Residue 99: ASN, Nonterminal, was not found in name map.)
> (Residue 100: LEU, Nonterminal, was not found in name map.)
> (Residue 101: ASP, Nonterminal, was not found in name map.)
> (Residue 102: ALA, Nonterminal, was not found in name map.)
> (Residue 103: LEU, Nonterminal, was not found in name map.)
> (Residue 104: HIS, Nonterminal, was not found in name map.)
> (Residue 105: ASP, Nonterminal, was not found in name map.)
> (Residue 106: HIS, Nonterminal, was not found in name map.)
> (Residue 107: LEU, Nonterminal, was not found in name map.)
> (Residue 108: ALA, Nonterminal, was not found in name map.)
> (Residue 109: THR, Nonterminal, was not found in name map.)
> (Residue 110: ILE, Nonterminal, was not found in name map.)
> (Residue 111: TYR, Nonterminal, was not found in name map.)
> (Residue 112: PRO, Nonterminal, was not found in name map.)
> (Residue 113: GLY, Nonterminal, was not found in name map.)
> (Residue 114: MET, Nonterminal, was not found in name map.)
> (Residue 115: ARG, Nonterminal, was not found in name map.)
> (Residue 116: ALA, Nonterminal, was not found in name map.)
> (Residue 117: PRO, Nonterminal, was not found in name map.)
> (Residue 118: SER, Nonterminal, was not found in name map.)
> (Residue 119: PHE, Nonterminal, was not found in name map.)
> (Residue 120: ARG, Nonterminal, was not found in name map.)
> (Residue 121: CYS, Nonterminal, was not found in name map.)
> (Residue 122: THR, Nonterminal, was not found in name map.)
> (Residue 123: ASP, Nonterminal, was not found in name map.)
> (Residue 124: ALA, Nonterminal, was not found in name map.)
> (Residue 125: GLU, Nonterminal, was not found in name map.)
> (Residue 126: LYS, Nonterminal, was not found in name map.)
> (Residue 127: GLY, Nonterminal, was not found in name map.)
> (Residue 128: LYS, Nonterminal, was not found in name map.)
> (Residue 129: GLY, Nonterminal, was not found in name map.)
> (Residue 130: LEU, Nonterminal, was not found in name map.)
> (Residue 131: ILE, Nonterminal, was not found in name map.)
> (Residue 132: LEU, Nonterminal, was not found in name map.)
> (Residue 133: HIS, Nonterminal, was not found in name map.)
> (Residue 134: TYR, Nonterminal, was not found in name map.)
> (Residue 135: TYR, Nonterminal, was not found in name map.)
> (Residue 136: SER, Nonterminal, was not found in name map.)
> (Residue 137: GLU, Nonterminal, was not found in name map.)
> (Residue 138: ARG, Nonterminal, was not found in name map.)
> (Residue 139: GLU, Nonterminal, was not found in name map.)
> (Residue 140: GLY, Nonterminal, was not found in name map.)
> (Residue 141: LEU, Nonterminal, was not found in name map.)
> (Residue 142: GLN, Nonterminal, was not found in name map.)
> (Residue 143: ASP, Nonterminal, was not found in name map.)
> (Residue 144: ILE, Nonterminal, was not found in name map.)
> (Residue 145: VAL, Nonterminal, was not found in name map.)
> (Residue 146: ILE, Nonterminal, was not found in name map.)
> (Residue 147: GLY, Nonterminal, was not found in name map.)
> (Residue 148: ILE, Nonterminal, was not found in name map.)
> (Residue 149: ILE, Nonterminal, was not found in name map.)
> (Residue 150: LYS, Nonterminal, was not found in name map.)
> (Residue 151: THR, Nonterminal, was not found in name map.)
> (Residue 152: VAL, Nonterminal, was not found in name map.)
> (Residue 153: ALA, Nonterminal, was not found in name map.)
> (Residue 154: GLN, Nonterminal, was not found in name map.)
> (Residue 155: GLN, Nonterminal, was not found in name map.)
> (Residue 156: ILE, Nonterminal, was not found in name map.)
> (Residue 157: HIS, Nonterminal, was not found in name map.)
> (Residue 158: GLY, Nonterminal, was not found in name map.)
> (Residue 159: THR, Nonterminal, was not found in name map.)
> (Residue 160: GLU, Nonterminal, was not found in name map.)
> (Residue 161: ILE, Nonterminal, was not found in name map.)
> (Residue 162: ASP, Nonterminal, was not found in name map.)
> (Residue 163: MET, Nonterminal, was not found in name map.)
> (Residue 164: LYS, Nonterminal, was not found in name map.)
> (Residue 165: VAL, Nonterminal, was not found in name map.)
> (Residue 166: ILE, Nonterminal, was not found in name map.)
> (Residue 167: GLN, Nonterminal, was not found in name map.)
> (Residue 168: GLN, Nonterminal, was not found in name map.)
> (Residue 169: ARG, Nonterminal, was not found in name map.)
> (Residue 170: ASN, Nonterminal, was not found in name map.)
> (Residue 171: GLU, Nonterminal, was not found in name map.)
> (Residue 172: GLU, Nonterminal, was not found in name map.)
> (Residue 173: CYS, Nonterminal, was not found in name map.)
> (Residue 174: ASP, Nonterminal, was not found in name map.)
> (Residue 175: HIS, Nonterminal, was not found in name map.)
> (Residue 176: THR, Nonterminal, was not found in name map.)
> (Residue 177: GLN, Nonterminal, was not found in name map.)
> (Residue 178: PHE, Nonterminal, was not found in name map.)
> (Residue 179: LEU, Nonterminal, was not found in name map.)
> (Residue 180: ILE, Nonterminal, was not found in name map.)
> (Residue 181: GLU, Nonterminal, was not found in name map.)
> (Residue 182: GLU, Nonterminal, was not found in name map.)
> (Residue 183: LYS, Nonterminal, was not found in name map.)
> (Residue 184: GLU, Nonterminal, was not found in name map.)
> Mapped residue SER, term: Terminal/last, seq. number: 185 to: CSER.
> (Residue 186: HEM, Terminal/last, was not found in name map.)
> Unknown residue: HEM number: 186 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Joining NMET - TYR
> Joining TYR - GLY
> Joining GLY - PHE
> Joining PHE - VAL
> Joining VAL - ASN
> Joining ASN - HIE
> Joining HIE - ALA
> Joining ALA - LEU
> Joining LEU - GLU
> Joining GLU - LEU
> Joining LEU - LEU
> Joining LEU - VAL
> Joining VAL - ILE
> Joining ILE - ARG
> Joining ARG - ASN
> Joining ASN - TYR
> Joining TYR - GLY
> Joining GLY - PRO
> Joining PRO - GLU
> Joining GLU - VAL
> Joining VAL - TRP
> Joining TRP - GLU
> Joining GLU - ASP
> Joining ASP - ILE
> Joining ILE - LYS
> Joining LYS - LYS
> Joining LYS - GLU
> Joining GLU - ALA
> Joining ALA - GLN
> Joining GLN - LEU
> Joining LEU - ASP
> Joining ASP - GLU
> Joining GLU - GLU
> Joining GLU - GLY
> Joining GLY - GLN
> Joining GLN - PHE
> Joining PHE - LEU
> Joining LEU - VAL
> Joining VAL - ARG
> Joining ARG - ILE
> Joining ILE - ILE
> Joining ILE - TYR
> Joining TYR - ASP
> Joining ASP - ASP
> Joining ASP - SER
> Joining SER - LYS
> Joining LYS - THR
> Joining THR - TYR
> Joining TYR - ASP
> Joining ASP - LEU
> Joining LEU - VAL
> Joining VAL - ALA
> Joining ALA - ALA
> Joining ALA - ALA
> Joining ALA - SER
> Joining SER - LYS
> Joining LYS - VAL
> Joining VAL - LEU
> Joining LEU - ASN
> Joining ASN - LEU
> Joining LEU - ASN
> Joining ASN - ALA
> Joining ALA - GLY
> Joining GLY - GLU
> Joining GLU - ILE
> Joining ILE - LEU
> Joining LEU - GLN
> Joining GLN - MET
> Joining MET - PHE
> Joining PHE - GLY
> Joining GLY - LYS
> Joining LYS - MET
> Joining MET - PHE
> Joining PHE - PHE
> Joining PHE - VAL
> Joining VAL - PHE
> Joining PHE - CYS
> Joining CYS - GLN
> Joining GLN - GLU
> Joining GLU - SER
> Joining SER - GLY
> Joining GLY - TYR
> Joining TYR - ASP
> Joining ASP - THR
> Joining THR - ILE
> Joining ILE - LEU
> Joining LEU - ARG
> Joining ARG - VAL
> Joining VAL - LEU
> Joining LEU - GLY
> Joining GLY - SER
> Joining SER - ASN
> Joining ASN - VAL
> Joining VAL - ARG
> Joining ARG - GLU
> Joining GLU - PHE
> Joining PHE - LEU
> Joining LEU - GLN
> Joining GLN - ASN
> Joining ASN - LEU
> Joining LEU - ASP
> Joining ASP - ALA
> Joining ALA - LEU
> Joining LEU - HIE
> Joining HIE - ASP
> Joining ASP - HIE
> Joining HIE - LEU
> Joining LEU - ALA
> Joining ALA - THR
> Joining THR - ILE
> Joining ILE - TYR
> Joining TYR - PRO
> Joining PRO - GLY
> Joining GLY - MET
> Joining MET - ARG
> Joining ARG - ALA
> Joining ALA - PRO
> Joining PRO - SER
> Joining SER - PHE
> Joining PHE - ARG
> Joining ARG - CYS
> Joining CYS - THR
> Joining THR - ASP
> Joining ASP - ALA
> Joining ALA - GLU
> Joining GLU - LYS
> Joining LYS - GLY
> Joining GLY - LYS
> Joining LYS - GLY
> Joining GLY - LEU
> Joining LEU - ILE
> Joining ILE - LEU
> Joining LEU - HIE
> Joining HIE - TYR
> Joining TYR - TYR
> Joining TYR - SER
> Joining SER - GLU
> Joining GLU - ARG
> Joining ARG - GLU
> Joining GLU - GLY
> Joining GLY - LEU
> Joining LEU - GLN
> Joining GLN - ASP
> Joining ASP - ILE
> Joining ILE - VAL
> Joining VAL - ILE
> Joining ILE - GLY
> Joining GLY - ILE
> Joining ILE - ILE
> Joining ILE - LYS
> Joining LYS - THR
> Joining THR - VAL
> Joining VAL - ALA
> Joining ALA - GLN
> Joining GLN - GLN
> Joining GLN - ILE
> Joining ILE - HIE
> Joining HIE - GLY
> Joining GLY - THR
> Joining THR - GLU
> Joining GLU - ILE
> Joining ILE - ASP
> Joining ASP - MET
> Joining MET - LYS
> Joining LYS - VAL
> Joining VAL - ILE
> Joining ILE - GLN
> Joining GLN - GLN
> Joining GLN - ARG
> Joining ARG - ASN
> Joining ASN - GLU
> Joining GLU - GLU
> Joining GLU - CYS
> Joining CYS - ASP
> Joining ASP - HIE
> Joining HIE - THR
> Joining THR - GLN
> Joining GLN - PHE
> Joining PHE - LEU
> Joining LEU - ILE
> Joining ILE - GLU
> Joining GLU - GLU
> Joining GLU - LYS
> Joining LYS - GLU
> Joining GLU - CSER
> Creating new UNIT for residue: HEM sequence: 187
> Created a new atom named: CAA within residue: .R<HEM 187>
> Created a new atom named: CAB within residue: .R<HEM 187>
> Created a new atom named: CAC within residue: .R<HEM 187>
> Created a new atom named: CAD within residue: .R<HEM 187>
> Created a new atom named: NA within residue: .R<HEM 187>
> Created a new atom named: CBA within residue: .R<HEM 187>
> Created a new atom named: CBB within residue: .R<HEM 187>
> Created a new atom named: CBC within residue: .R<HEM 187>
> Created a new atom named: CBD within residue: .R<HEM 187>
> Created a new atom named: NB within residue: .R<HEM 187>
> Created a new atom named: CGA within residue: .R<HEM 187>
> Created a new atom named: CGD within residue: .R<HEM 187>
> Created a new atom named: ND within residue: .R<HEM 187>
> Created a new atom named: CHA within residue: .R<HEM 187>
> Created a new atom named: CHB within residue: .R<HEM 187>
> Created a new atom named: CHC within residue: .R<HEM 187>
> Created a new atom named: CHD within residue: .R<HEM 187>
> Created a new atom named: CMA within residue: .R<HEM 187>
> Created a new atom named: CMB within residue: .R<HEM 187>
> Created a new atom named: CMC within residue: .R<HEM 187>
> Created a new atom named: CMD within residue: .R<HEM 187>
> Created a new atom named: C1A within residue: .R<HEM 187>
> Created a new atom named: C1B within residue: .R<HEM 187>
> Created a new atom named: C1C within residue: .R<HEM 187>
> Created a new atom named: C1D within residue: .R<HEM 187>
> Created a new atom named: O01 within residue: .R<HEM 187>
> Created a new atom named: O1A within residue: .R<HEM 187>
> Created a new atom named: O1D within residue: .R<HEM 187>
> Created a new atom named: C2A within residue: .R<HEM 187>
> Created a new atom named: C2B within residue: .R<HEM 187>
> Created a new atom named: C2C within residue: .R<HEM 187>
> Created a new atom named: C2D within residue: .R<HEM 187>
> Created a new atom named: O02 within residue: .R<HEM 187>
> Created a new atom named: O2A within residue: .R<HEM 187>
> Created a new atom named: O2D within residue: .R<HEM 187>
> Created a new atom named: C3A within residue: .R<HEM 187>
> Created a new atom named: C3B within residue: .R<HEM 187>
> Created a new atom named: C3C within residue: .R<HEM 187>
> Created a new atom named: C3D within residue: .R<HEM 187>
> Created a new atom named: C4A within residue: .R<HEM 187>
> Created a new atom named: C4B within residue: .R<HEM 187>
> Created a new atom named: C4C within residue: .R<HEM 187>
> Created a new atom named: C4D within residue: .R<HEM 187>
> Created a new atom named: NC within residue: .R<HEM 187>
> Created a new atom named: FE within residue: .R<HEM 187>
> total atoms in file: 1547
> Leap added 1479 missing atoms according to residue templates:
> 1479 H / lone pairs
> The file contained 45 atoms not in residue templates
> > saveamberparm complex 1FKO_sus.prmtop 1FKO_sus.inpcrd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -12.000000 is not zero.
> FATAL: Atom .R<HEM 187>.A<CAA 1> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CAB 2> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CAC 3> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CAD 4> does not have a type.
> FATAL: Atom .R<HEM 187>.A<NA 5> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CBA 6> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CBB 7> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CBC 8> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CBD 9> does not have a type.
> FATAL: Atom .R<HEM 187>.A<NB 10> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CGA 11> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CGD 12> does not have a type.
> FATAL: Atom .R<HEM 187>.A<ND 13> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CHA 14> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CHB 15> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CHC 16> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CHD 17> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CMA 18> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CMB 19> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CMC 20> does not have a type.
> FATAL: Atom .R<HEM 187>.A<CMD 21> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C1A 22> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C1B 23> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C1C 24> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C1D 25> does not have a type.
> FATAL: Atom .R<HEM 187>.A<O01 26> does not have a type.
> FATAL: Atom .R<HEM 187>.A<O1A 27> does not have a type.
> FATAL: Atom .R<HEM 187>.A<O1D 28> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C2A 29> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C2B 30> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C2C 31> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C2D 32> does not have a type.
> FATAL: Atom .R<HEM 187>.A<O02 33> does not have a type.
> FATAL: Atom .R<HEM 187>.A<O2A 34> does not have a type.
> FATAL: Atom .R<HEM 187>.A<O2D 35> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C3A 36> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C3B 37> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C3C 38> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C3D 39> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C4A 40> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C4B 41> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C4C 42> does not have a type.
> FATAL: Atom .R<HEM 187>.A<C4D 43> does not have a type.
> FATAL: Atom .R<HEM 187>.A<NC 44> does not have a type.
> FATAL: Atom .R<HEM 187>.A<FE 45> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
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--
====================================================================
David A. Case | david.case.rutgers.edu
Dept. of Chemistry & Chemical Biology |
Rutgers University | office: +1-848-445-5885
174 Frelinghuysen Road, Rm. 208b | cell: +1-609-751-8668
Piscataway, NJ 08854 USA | http://casegroup.rutgers.edu
====================================================================
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Received on Thu Jun 29 2017 - 07:30:02 PDT
