antechamber:
1

Welcome to antechamber: molecular input file processor.

Warning: Detected more than 10 Residue sequence numbers;
         this may be a large multiple residue PDB file;
         large multiple residue PDB files are not supported.
         Continuing, but problems may be encountered.
/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Invalid atom id (9) in line (CONECT    1    9   21   22   23                                       
).

<***************>
parmchk2:
1
Cannot open file (updated_alatis_output_compound_sdf.mol2) with mode (r).No such file or directory

<***************>
tleap:
0
-I: Adding /usr/software/amber16/dat/leap/prep to search path.
-I: Adding /usr/software/amber16/dat/leap/lib to search path.
-I: Adding /usr/software/amber16/dat/leap/parm to search path.
-I: Adding /usr/software/amber16/dat/leap/cmd to search path.
-f: Source tleap.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap.in
----- Source: /usr/software/amber16/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /usr/software/amber16/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /usr/software/amber16/dat/leap/lib/amino12.lib
Loading library: /usr/software/amber16/dat/leap/lib/aminoct12.lib
Loading library: /usr/software/amber16/dat/leap/lib/aminont12.lib
----- Source: /usr/software/amber16/dat/leap/cmd/leaprc.gaff
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
Could not open file updated_alatis_output_compound_sdf.mol2: not found
check: Argument #1 is type String must be of type: [unit molecule residue atom]
usage:  check <unit> [parmset]
Could not open file updated_alatis_output_compound_sdf.frcmod: not found
check: Argument #1 is type String must be of type: [unit molecule residue atom]
usage:  check <unit> [parmset]
saveOff: Argument #1 is type String must be of type: [unit parameter_set list]
usage:  saveOff <object> <filename>
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage:  saveAmberParm <unit> <topologyfile> <coordfile> 
	Quit

<***************>
charmm:
1

Welcome to antechamber: molecular input file processor.

/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot open file (updated_alatis_output_compound_sdf.mol2) with mode (r).No such file or directory

<***************>
antechamber:
1

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Atom IDs must be in Columns 7-11.

<***************>
parmchk2:
1
Cannot open file (updated_alatis_output_compound_sdf.mol2) with mode (r).
No such file or directory

<***************>
tleap:
0
-I: Adding /usr/software/amber16/dat/leap/prep to search path.
-I: Adding /usr/software/amber16/dat/leap/lib to search path.
-I: Adding /usr/software/amber16/dat/leap/parm to search path.
-I: Adding /usr/software/amber16/dat/leap/cmd to search path.
-f: Source tleap.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap.in
----- Source: /usr/software/amber16/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /usr/software/amber16/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /usr/software/amber16/dat/leap/lib/amino12.lib
Loading library: /usr/software/amber16/dat/leap/lib/aminoct12.lib
Loading library: /usr/software/amber16/dat/leap/lib/aminont12.lib
----- Source: /usr/software/amber16/dat/leap/cmd/leaprc.gaff
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
Could not open file updated_alatis_output_compound_sdf.mol2: not found
check: Argument #1 is type String must be of type: [unit molecule residue atom]
usage:  check <unit> [parmset]
Could not open file updated_alatis_output_compound_sdf.frcmod: not found
check: Argument #1 is type String must be of type: [unit molecule residue atom]
usage:  check <unit> [parmset]
saveOff: Argument #1 is type String must be of type: [unit parameter_set list]
usage:  saveOff <object> <filename>
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage:  saveAmberParm <unit> <topologyfile> <coordfile> 
	Quit

<***************>
charmm:
1

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot open the input file (updated_alatis_output_compound_sdf.mol2).
No such file or directory

<***************>
antechamber:
1

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Atom IDs must be in Columns 7-11.

<***************>
parmchk2:
1
Cannot open file (updated_alatis_output_compound_sdf.mol2) with mode (r).
No such file or directory

<***************>
tleap:
0
-I: Adding /usr/software/amber16/dat/leap/prep to search path.
-I: Adding /usr/software/amber16/dat/leap/lib to search path.
-I: Adding /usr/software/amber16/dat/leap/parm to search path.
-I: Adding /usr/software/amber16/dat/leap/cmd to search path.
-f: Source tleap.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap.in
----- Source: /usr/software/amber16/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /usr/software/amber16/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /usr/software/amber16/dat/leap/lib/amino12.lib
Loading library: /usr/software/amber16/dat/leap/lib/aminoct12.lib
Loading library: /usr/software/amber16/dat/leap/lib/aminont12.lib
----- Source: /usr/software/amber16/dat/leap/cmd/leaprc.gaff
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
Could not open file updated_alatis_output_compound_sdf.mol2: not found
check: Argument #1 is type String must be of type: [unit molecule residue atom]
usage:  check <unit> [parmset]
Could not open file updated_alatis_output_compound_sdf.frcmod: not found
check: Argument #1 is type String must be of type: [unit molecule residue atom]
usage:  check <unit> [parmset]
saveOff: Argument #1 is type String must be of type: [unit parameter_set list]
usage:  saveOff <object> <filename>
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage:  saveAmberParm <unit> <topologyfile> <coordfile> 
	Quit

<***************>
charmm:
1

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot open the input file (updated_alatis_output_compound_sdf.mol2).
No such file or directory

<***************>
antechamber:
1

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Atom IDs must be in Columns 7-11.

<***************>
parmchk2:
1
Cannot open file (updated_alatis_output_compound_sdf.mol2) with mode (r).
No such file or directory

<***************>
tleap:
0
-I: Adding /usr/software/amber16/dat/leap/prep to search path.
-I: Adding /usr/software/amber16/dat/leap/lib to search path.
-I: Adding /usr/software/amber16/dat/leap/parm to search path.
-I: Adding /usr/software/amber16/dat/leap/cmd to search path.
-f: Source tleap.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap.in
----- Source: /usr/software/amber16/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /usr/software/amber16/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /usr/software/amber16/dat/leap/lib/amino12.lib
Loading library: /usr/software/amber16/dat/leap/lib/aminoct12.lib
Loading library: /usr/software/amber16/dat/leap/lib/aminont12.lib
----- Source: /usr/software/amber16/dat/leap/cmd/leaprc.gaff
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
Could not open file updated_alatis_output_compound_sdf.mol2: not found
check: Argument #1 is type String must be of type: [unit molecule residue atom]
usage:  check <unit> [parmset]
Could not open file updated_alatis_output_compound_sdf.frcmod: not found
check: Argument #1 is type String must be of type: [unit molecule residue atom]
usage:  check <unit> [parmset]
saveOff: Argument #1 is type String must be of type: [unit parameter_set list]
usage:  saveOff <object> <filename>
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage:  saveAmberParm <unit> <topologyfile> <coordfile> 
	Quit

<***************>
charmm:
1

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot open the input file (updated_alatis_output_compound_sdf.mol2).
No such file or directory

<***************>
antechamber:
0

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
   Status: pass
Warning: Detected more than 10 Residue sequence numbers;
         this may be a large multiple residue PDB file;
         large multiple residue PDB files are not supported.
         Continuing, but problems may be encountered.
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded   
      for those not bonded   
   Status: pass
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Running: /usr/software/amber16/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

---Judge bond type for Residue 1 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 2 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 3 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 4 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 5 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 6 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 7 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 8 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 9 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 10 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 11 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 12 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 13 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 14 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 15 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 16 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 17 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 18 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 19 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 20 with ID of 2 and Name of TYR ---

Running: /usr/software/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 144; net charge: 0

Running: /usr/software/amber16/bin/sqm -O -i sqm.in -o sqm.out

Running: /usr/software/amber16/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/software/amber16/dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /usr/software/amber16/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC


<***************>
parmchk2:
0

<***************>
tleap:
0
-I: Adding /usr/software/amber16/dat/leap/prep to search path.
-I: Adding /usr/software/amber16/dat/leap/lib to search path.
-I: Adding /usr/software/amber16/dat/leap/parm to search path.
-I: Adding /usr/software/amber16/dat/leap/cmd to search path.
-f: Source tleap.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap.in
----- Source: /usr/software/amber16/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /usr/software/amber16/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /usr/software/amber16/dat/leap/lib/amino12.lib
Loading library: /usr/software/amber16/dat/leap/lib/aminoct12.lib
Loading library: /usr/software/amber16/dat/leap/lib/aminont12.lib
----- Source: /usr/software/amber16/dat/leap/cmd/leaprc.gaff
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
Loading Mol2 file: ./updated_alatis_output_compound_sdf.mol2
Reading MOLECULE named LEU
Checking 'updated_alatis_output_compound_sdf'....
Checking parameters for unit 'updated_alatis_output_compound_sdf'.
Checking for bond parameters.
Checking for angle parameters.
Could not find angle parameter: ce - cd - c
There are missing parameters.
Unit is OK.
Loading parameters: ./updated_alatis_output_compound_sdf.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Checking 'updated_alatis_output_compound_sdf'....
Checking parameters for unit 'updated_alatis_output_compound_sdf'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
 Creating updated_alatis_output_compound_sdf.lib
Building topology.
Building atom parameters.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 14 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

	LEU	1
  )
 (no restraints)
	Quit

<***************>
charmm:
0

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 File --
   Status: pass
Info: Finished reading file (updated_alatis_output_compound_sdf.mol2).
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded   
      for those not bonded   
   Status: pass
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Running: /usr/software/amber16/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

---Judge bond type for Residue 1 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 2 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 3 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 4 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 5 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 6 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 7 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 8 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 9 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 10 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 11 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 12 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 13 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 14 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 15 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 16 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 17 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 18 with ID of 2 and Name of TYR ---

---Judge bond type for Residue 19 with ID of 1 and Name of LEU ---

---Judge bond type for Residue 20 with ID of 2 and Name of TYR ---

Running: /usr/software/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Running: /usr/software/amber16/bin/atomtype -i ANTECHAMBER_PREP.AC0 -o ANTECHAMBER_PREP.AC -p gaff

Running: /usr/software/amber16/bin/charmmgen -i ANTECHAMBER_PREP.AC -f ac -o updated_alatis_output_compound_sdf.charmm -r MOL


<***************>
