log started: Tue Dec 31 12:50:54 2024

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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named MOL
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod 
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	MOL	1
  )
 (no restraints)
> #savepdb com complex.pdb 
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge com
> #addIons com Na+ 0.0
> #charge com
> #solvateOct com TIP3PBOX 10.0
> #savepdb com complex-solv.pdb 
> #saveamberparm com complex-solv.prmtop complex-solv.inpcrd
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
log started: Tue Dec 31 12:56:18 2024

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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod 
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	MOL	1
  )
 (no restraints)
> #savepdb com complex.pdb 
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge com
> #addIons com Na+ 0.0
> #charge com
> #solvateOct com TIP3PBOX 10.0
> #savepdb com complex-solv.pdb 
> #saveamberparm com complex-solv.prmtop complex-solv.inpcrd
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
log started: Tue Dec 31 13:00:46 2024

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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod 
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	MOL	1
  )
 (no restraints)
> #savepdb com complex.pdb 
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge com
> #addIons com Na+ 0.0
> #charge com
> #solvateOct com TIP3PBOX 10.0
> #savepdb com complex-solv.pdb 
> #saveamberparm com complex-solv.prmtop complex-solv.inpcrd
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
log started: Tue Dec 31 13:01:22 2024

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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod 
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	MOL	1
  )
 (no restraints)
> #savepdb com complex.pdb 
> #saveamberparm com complex.prmtop complex.inpcrd
> charge ligand
Total unperturbed charge:  -0.000000
Total perturbed charge:    -0.000000
> #addIons com Na+ 0.0
> #charge com
> #solvateOct com TIP3PBOX 10.0
> #savepdb com complex-solv.pdb 
> #saveamberparm com complex-solv.prmtop complex-solv.inpcrd
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
log started: Tue Dec 31 13:02:26 2024

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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod 
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	MOL	1
  )
 (no restraints)
> #savepdb com complex.pdb 
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge ligand
> #addIons com Na+ 0.0
> #charge com
> solvateBox ligand OPC3BOX 10.0
  Solute vdw bounding box:              7.058 6.274 3.721
  Total bounding box for atom centers:  27.058 26.274 23.721
  Solvent unit box:                     18.682 18.750 18.542
The number of boxes:  x= 2  y= 2  z= 2
  Total vdw box size:                   30.224 29.482 26.639 angstroms.
  Volume: 23737.147 A^3 
  Total mass 5497.978 amu,  Density 0.385 g/cc
  Added 493 residues.
> savepdb ligand lig-solv.pdb 
Writing pdb file: lig-solv.pdb
   printing CRYST1 record to PDB file with box info
> saveamberparm com complex-solv.prmtop complex-solv.inpcrd

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Fatal Error!
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage:  saveAmberParm <unit> <topologyfile> <coordfile> 

Exiting LEaP: Errors = 1; Warnings = 0; Notes = 0.
log started: Tue Dec 31 13:06:47 2024

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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod 
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	MOL	1
  )
 (no restraints)
> #savepdb com complex.pdb 
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge ligand
> #addIons com Na+ 0.0
> #charge com
> solvateBox ligand OPC3BOX 10.0
  Solute vdw bounding box:              7.058 6.274 3.721
  Total bounding box for atom centers:  27.058 26.274 23.721
  Solvent unit box:                     18.682 18.750 18.542
The number of boxes:  x= 2  y= 2  z= 2
  Total vdw box size:                   30.224 29.482 26.639 angstroms.
  Volume: 23737.147 A^3 
  Total mass 5497.978 amu,  Density 0.385 g/cc
  Added 493 residues.
> savepdb ligand lig-solv.pdb 
Writing pdb file: lig-solv.pdb
   printing CRYST1 record to PDB file with box info
> saveamberparm ligand lig-solv.prmtop lig-solv.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	MOL	1
	WAT	493
  )
 (no restraints)
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
log started: Tue Dec 31 13:08:44 2024

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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod 
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	PYR	1
  )
 (no restraints)
> #savepdb com complex.pdb 
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge ligand
> #addIons com Na+ 0.0
> #charge com
> solvateBox ligand OPC3BOX 10.0
  Solute vdw bounding box:              7.058 6.274 3.721
  Total bounding box for atom centers:  27.058 26.274 23.721
  Solvent unit box:                     18.682 18.750 18.542
The number of boxes:  x= 2  y= 2  z= 2
  Total vdw box size:                   30.224 29.482 26.639 angstroms.
  Volume: 23737.147 A^3 
  Total mass 5497.978 amu,  Density 0.385 g/cc
  Added 493 residues.
> savepdb ligand lig-solv.pdb 
Writing pdb file: lig-solv.pdb
   printing CRYST1 record to PDB file with box info
> saveamberparm ligand lig-solv.prmtop lig-solv.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	PYR	1
	WAT	493
  )
 (no restraints)
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
log started: Mon Jan  6 12:46:18 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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod 
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	PYR	1
  )
 (no restraints)
> #savepdb com complex.pdb 
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge ligand
> #addIons com Na+ 0.0
> #charge com
> solvateBox ligand OPC3BOX 15.0
  Solute vdw bounding box:              7.058 6.274 3.721
  Total bounding box for atom centers:  37.058 36.274 33.721
  Solvent unit box:                     18.682 18.750 18.542
The number of boxes:  x= 2  y= 2  z= 2
  Total vdw box size:                   40.158 39.686 36.806 angstroms.
  Volume: 58658.280 A^3 
  Total mass 15522.538 amu,  Density 0.439 g/cc
  Added 1403 residues.
> savepdb ligand lig-solv.pdb 
Writing pdb file: lig-solv.pdb
   printing CRYST1 record to PDB file with box info
> saveamberparm ligand lig-solv.prmtop lig-solv.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	PYR	1
	WAT	1403
  )
 (no restraints)
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
log started: Mon Jan  6 15:14:12 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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod 
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	PYR	1
  )
 (no restraints)
> #savepdb com complex.pdb 
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge ligand
> #addIons com Na+ 0.0
> #charge com
> solvateBox ligand OPC3BOX 30.0
  Solute vdw bounding box:              7.058 6.274 3.721
  Total bounding box for atom centers:  67.058 66.274 63.721
  Solvent unit box:                     18.682 18.750 18.542
The number of boxes:  x= 4  y= 4  z= 4
  Total vdw box size:                   70.325 69.299 67.057 angstroms.
  Volume: 326800.783 A^3 
  Total mass 100896.538 amu,  Density 0.513 g/cc
  Added 9153 residues.
> savepdb ligand lig-solv.pdb 
Writing pdb file: lig-solv.pdb
   printing CRYST1 record to PDB file with box info
> saveamberparm ligand lig-solv.prmtop lig-solv.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	PYR	1
	WAT	9153
  )
 (no restraints)
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
log started: Thu Jan  9 23:48:16 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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> #saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
> #savepdb com complex.pdb
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge ligand
> #addIons com Na+ 0.0
> #charge com
> mol =loadpdb lig-solv.pdb
Loading PDB file: ./lig-solv.pdb
Matching PDB residue names to LEaP variables.

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Warning!
Unknown residue: PYR   number: 0   type: Terminal/last
..relaxing end constraints to try for a dbase match

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Warning!
  -no luck
Creating new UNIT for residue: PYR sequence: 1
Created a new atom named: C within residue: .R<PYR 1>
Created a new atom named: C1 within residue: .R<PYR 1>
Created a new atom named: C2 within residue: .R<PYR 1>
Created a new atom named: C3 within residue: .R<PYR 1>
Created a new atom named: N within residue: .R<PYR 1>
Created a new atom named: H within residue: .R<PYR 1>
Created a new atom named: H1 within residue: .R<PYR 1>
Created a new atom named: H2 within residue: .R<PYR 1>
Created a new atom named: H3 within residue: .R<PYR 1>
Created a new atom named: H4 within residue: .R<PYR 1>
  total atoms in file: 27469
  The file contained 10 atoms not in residue templates
> setbox mol vdw 
 (using default radius 1.500000 for C)
 (using default radius 1.500000 for C1)
 (using default radius 1.500000 for C2)
 (using default radius 1.500000 for C3)
 (using default radius 1.500000 for N)
Box dimensions:  70.296600 69.270600 67.028600
> ; Save topology and coordinates

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Fatal Error!
Error from the parser: 
       syntax error.
       Check for typos, misspellings, etc.
       Try help on the command name and desc on the command arguments.

Exiting LEaP: Errors = 1; Warnings = 2; Notes = 0.
log started: Thu Jan  9 23:49:38 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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> #saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
> #savepdb com complex.pdb
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge ligand
> #addIons com Na+ 0.0
> #charge com
> mol =loadpdb lig-solv.pdb
Loading PDB file: ./lig-solv.pdb
Matching PDB residue names to LEaP variables.

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Warning!
Unknown residue: PYR   number: 0   type: Terminal/last
..relaxing end constraints to try for a dbase match

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Warning!
  -no luck
Creating new UNIT for residue: PYR sequence: 1
Created a new atom named: C within residue: .R<PYR 1>
Created a new atom named: C1 within residue: .R<PYR 1>
Created a new atom named: C2 within residue: .R<PYR 1>
Created a new atom named: C3 within residue: .R<PYR 1>
Created a new atom named: N within residue: .R<PYR 1>
Created a new atom named: H within residue: .R<PYR 1>
Created a new atom named: H1 within residue: .R<PYR 1>
Created a new atom named: H2 within residue: .R<PYR 1>
Created a new atom named: H3 within residue: .R<PYR 1>
Created a new atom named: H4 within residue: .R<PYR 1>
  total atoms in file: 27469
  The file contained 10 atoms not in residue templates
> setbox mol vdw 
 (using default radius 1.500000 for C)
 (using default radius 1.500000 for C1)
 (using default radius 1.500000 for C2)
 (using default radius 1.500000 for C3)
 (using default radius 1.500000 for N)
Box dimensions:  70.296600 69.270600 67.028600
> ; Save topology and coordinates

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Fatal Error!
Error from the parser: 
       syntax error.
       Check for typos, misspellings, etc.
       Try help on the command name and desc on the command arguments.

Exiting LEaP: Errors = 1; Warnings = 2; Notes = 0.
log started: Thu Jan  9 23:53:39 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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> #saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
> #savepdb com complex.pdb
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge ligand
> #addIons com Na+ 0.0
> #charge com
> mol =loadpdb lig-solv.pdb
Loading PDB file: ./lig-solv.pdb
Matching PDB residue names to LEaP variables.

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Warning!
Unknown residue: PYR   number: 0   type: Terminal/last
..relaxing end constraints to try for a dbase match

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Warning!
  -no luck
Creating new UNIT for residue: PYR sequence: 1
Created a new atom named: C within residue: .R<PYR 1>
Created a new atom named: C1 within residue: .R<PYR 1>
Created a new atom named: C2 within residue: .R<PYR 1>
Created a new atom named: C3 within residue: .R<PYR 1>
Created a new atom named: N within residue: .R<PYR 1>
Created a new atom named: H within residue: .R<PYR 1>
Created a new atom named: H1 within residue: .R<PYR 1>
Created a new atom named: H2 within residue: .R<PYR 1>
Created a new atom named: H3 within residue: .R<PYR 1>
Created a new atom named: H4 within residue: .R<PYR 1>
  total atoms in file: 27469
  The file contained 10 atoms not in residue templates
> setbox mol vdw 
 (using default radius 1.500000 for C)
 (using default radius 1.500000 for C1)
 (using default radius 1.500000 for C2)
 (using default radius 1.500000 for C3)
 (using default radius 1.500000 for N)
Box dimensions:  70.296600 69.270600 67.028600
> 
> #set pname lig-solv-qmmm.prmtop
> #set iname lig-solv-qmmm.inpcrd
> #saveoff pname piname
> #solvateBox ligand OPC3BOX 30.0
> #savepdb ligand lig-solv.pdb
> saveamberparm ligand lig-solv-qmmm.prmtop lig-solv-qmmm.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	PYR	1
  )
 (no restraints)
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 2; Notes = 0.
log started: Thu Jan  9 23:59:13 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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> #saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
> #savepdb com complex.pdb
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge ligand
> #addIons com Na+ 0.0
> #charge com
> mol =loadpdb lig-solv.pdb
Loading PDB file: ./lig-solv.pdb
Matching PDB residue names to LEaP variables.

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Warning!
Unknown residue: PYR   number: 0   type: Terminal/last
..relaxing end constraints to try for a dbase match

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Warning!
  -no luck
Creating new UNIT for residue: PYR sequence: 1
Created a new atom named: C within residue: .R<PYR 1>
Created a new atom named: C1 within residue: .R<PYR 1>
Created a new atom named: C2 within residue: .R<PYR 1>
Created a new atom named: C3 within residue: .R<PYR 1>
Created a new atom named: N within residue: .R<PYR 1>
Created a new atom named: H within residue: .R<PYR 1>
Created a new atom named: H1 within residue: .R<PYR 1>
Created a new atom named: H2 within residue: .R<PYR 1>
Created a new atom named: H3 within residue: .R<PYR 1>
Created a new atom named: H4 within residue: .R<PYR 1>
  total atoms in file: 27469
  The file contained 10 atoms not in residue templates
> #setbox mol vdw 
> 
> #set pname lig-solv-qmmm.prmtop
> #set iname lig-solv-qmmm.inpcrd
> #saveoff pname piname
> #solvateBox ligand OPC3BOX 30.0
> #savepdb ligand lig-solv.pdb
> saveamberparm ligand lig-solv-qmmm.prmtop lig-solv-qmmm.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	PYR	1
  )
 (no restraints)
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 2; Notes = 0.
log started: Fri Jan 10 00:19:03 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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod 
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	PYR	1
  )
 (no restraints)
> #savepdb com complex.pdb 
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge ligand
> #addIons com Na+ 0.0
> #charge com
> #solvateBox ligand OPC3BOX 30.0
> #savepdb ligand lig-solv.pdb 
> #saveamberparm ligand lig-solv.prmtop lig-solv.inpcrd
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
log started: Fri Jan 10 10:03:08 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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> #loadamberparams EAI045.frcmod 
> 
> #charge protein
> #com = combine {protein ligand}
> 
> #saveamberparm protein 1m17.prmtop 1m17.inpcrd
> saveamberparm ligand pyrrole.prmtop pyrrole.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	PYR	1
  )
 (no restraints)
> #savepdb com complex.pdb 
> #saveamberparm com complex.prmtop complex.inpcrd
> #charge ligand
> #addIons com Na+ 0.0
> #charge com
> #solvateBox ligand OPC3BOX 30.0
> #savepdb ligand lig-solv.pdb 
> #saveamberparm ligand lig-solv.prmtop lig-solv.inpcrd
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
log started: Fri Jan 10 10:03:47 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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> mol =loadpdb equil.pdb
Loading PDB file: ./equil.pdb
Matching PDB residue names to LEaP variables.

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Warning!
Unknown residue: PYR   number: 0   type: Terminal/last
..relaxing end constraints to try for a dbase match

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Warning!
  -no luck
Creating new UNIT for residue: PYR sequence: 1
Created a new atom named: C within residue: .R<PYR 1>
Created a new atom named: C1 within residue: .R<PYR 1>
Created a new atom named: C2 within residue: .R<PYR 1>
Created a new atom named: C3 within residue: .R<PYR 1>
Created a new atom named: N within residue: .R<PYR 1>
Created a new atom named: H within residue: .R<PYR 1>
Created a new atom named: H1 within residue: .R<PYR 1>
Created a new atom named: H2 within residue: .R<PYR 1>
Created a new atom named: H3 within residue: .R<PYR 1>
Created a new atom named: H4 within residue: .R<PYR 1>
  total atoms in file: 1489
  The file contained 10 atoms not in residue templates
> setbox mol vdw 
 (using default radius 1.500000 for C)
 (using default radius 1.500000 for C1)
 (using default radius 1.500000 for C2)
 (using default radius 1.500000 for C3)
 (using default radius 1.500000 for N)
Box dimensions:  32.039300 31.310300 28.104300
> saveamberparm ligand lig-solv-qmmm.prmtop lig-solv-qmmm.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	PYR	1
  )
 (no restraints)
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 2; Notes = 0.
log started: Fri Jan 10 10:15:49 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: /apps/scratch/compile/amber22/amber22_cpu_mpi/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams pyrrole.frcmod
Loading parameters: ./pyrrole.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ligand =loadmol2 pyrrole.mol2
Loading Mol2 file: ./pyrrole.mol2
Reading MOLECULE named PYR
> check ligand
Checking 'ligand'....
Checking parameters for unit 'ligand'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> mol =loadpdb equil.pdb
Loading PDB file: ./equil.pdb
Matching PDB residue names to LEaP variables.

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Warning!
Unknown residue: PYR   number: 0   type: Terminal/last
..relaxing end constraints to try for a dbase match

/apps/scratch/compile/amber22/amber22_cpu_mpi/bin/teLeap: Warning!
  -no luck
Creating new UNIT for residue: PYR sequence: 1
Created a new atom named: C within residue: .R<PYR 1>
Created a new atom named: C1 within residue: .R<PYR 1>
Created a new atom named: C2 within residue: .R<PYR 1>
Created a new atom named: C3 within residue: .R<PYR 1>
Created a new atom named: N within residue: .R<PYR 1>
Created a new atom named: H within residue: .R<PYR 1>
Created a new atom named: H1 within residue: .R<PYR 1>
Created a new atom named: H2 within residue: .R<PYR 1>
Created a new atom named: H3 within residue: .R<PYR 1>
Created a new atom named: H4 within residue: .R<PYR 1>
  total atoms in file: 1489
  The file contained 10 atoms not in residue templates
> setbox mol vdw 
 (using default radius 1.500000 for C)
 (using default radius 1.500000 for C1)
 (using default radius 1.500000 for C2)
 (using default radius 1.500000 for C3)
 (using default radius 1.500000 for N)
Box dimensions:  32.039300 31.310300 28.104300
> saveamberparm ligand lig-solv-qmmm.prmtop lig-solv-qmmm.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 5 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

	PYR	1
  )
 (no restraints)
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 2; Notes = 0.