chianina.nmrfam.wisc.edu

command from alatis:
	/opt/amber16/bin/antechamber -i updated_alatis_output_bmse000786_mol.pdb -fi pdb -o  updated_alatis_output_bmse000786_mol.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 --
Warning: Unusual element (As) for atom (ID: 3, Name: As03).
GAFF does not have sufficient parameters for molecules having unusual
         elements (those other than H,C,N,O,S,P and halogens).
         To ensure antechamber works properly, one may need to designate
         bond types for bonds involved with unusual elements.
         To do so, simply freeze the bond types by appending "F" or "f" 
         to the corresponding bond types in ac or mol2 files.
-- 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: /opt/amber16/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Warning: For atom (ID: 3, Name: As03) the best APS is not zero.
         Bonds involving this atom are frozen.
The frozen atom type can only be 1, 2, 3, 7 (aromatic single),
or 8 (aromatic double).
/opt/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot properly run "/opt/amber16/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac".

<***************>
parmchk2:
1
Cannot open file (updated_alatis_output_bmse000786_mol.mol2) with mode (r).
No such file or directory

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

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap.in
----- Source: /opt/amber16/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /opt/amber16/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /opt/amber16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /opt/amber16/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /opt/amber16/dat/leap/lib/amino12.lib
Loading library: /opt/amber16/dat/leap/lib/aminoct12.lib
Loading library: /opt/amber16/dat/leap/lib/aminont12.lib
----- Source: /opt/amber16/dat/leap/cmd/leaprc.gaff
----- Source of /opt/amber16/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /opt/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_bmse000786_mol.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_bmse000786_mol.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.
/opt/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot open the input file (updated_alatis_output_bmse000786_mol.mol2).
No such file or directory

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