v4-0h07-0

command from alatis:
	antechamber -i updated_alatis_output_compound_3D_h_sdf.pdb -fi pdb -o  updated_alatis_output_compound_3D_h_sdf.mol2 -fo mol2 -c bcc -s 2
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 --
   Status: pass
-- 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

Running: /usr/software/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 57; net charge: 0
Info: The number of electrons is odd (57).
      Please check the total charge (-nc flag) and spin multiplicity (-m flag).

Running: /usr/software/amber16/bin/sqm -O -i sqm.in -o sqm.out
/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot properly run "/usr/software/amber16/bin/sqm -O -i sqm.in -o sqm.out".

<***************>
parmchk2:
1
Cannot open file (updated_alatis_output_compound_3D_h_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_3D_h_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_3D_h_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_3D_h_sdf.mol2).
No such file or directory

<***************>
v4-0h07-0

command from alatis:
	antechamber -i updated_alatis_output_compound_3D_h_sdf.pdb -fi pdb -o  updated_alatis_output_compound_3D_h_sdf.mol2 -fo mol2 -c bcc -s 2
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 --
   Status: pass
-- 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

Running: /usr/software/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 57; net charge: 0
Info: The number of electrons is odd (57).
      Please check the total charge (-nc flag) and spin multiplicity (-m flag).

Running: /usr/software/amber16/bin/sqm -O -i sqm.in -o sqm.out
/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot properly run "/usr/software/amber16/bin/sqm -O -i sqm.in -o sqm.out".

<***************>
parmchk2:
1
Cannot open file (updated_alatis_output_compound_3D_h_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_3D_h_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_3D_h_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_3D_h_sdf.mol2).
No such file or directory

<***************>
v4-0h07-0

command from alatis:
	antechamber -i updated_alatis_output_compound_3D_h_sdf.pdb -fi pdb -o  updated_alatis_output_compound_3D_h_sdf.mol2 -fo mol2 -c bcc -s 2
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 --
   Status: pass
-- 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

Running: /usr/software/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 57; net charge: 0
Info: The number of electrons is odd (57).
      Please check the total charge (-nc flag) and spin multiplicity (-m flag).

Running: /usr/software/amber16/bin/sqm -O -i sqm.in -o sqm.out
/usr/software/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot properly run "/usr/software/amber16/bin/sqm -O -i sqm.in -o sqm.out".

<***************>
parmchk2:
1
Cannot open file (updated_alatis_output_compound_3D_h_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_3D_h_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_3D_h_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_3D_h_sdf.mol2).
No such file or directory

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