antechamber:
0

Welcome to antechamber: 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: 58; 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


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parmchk2:
0

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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 UNL
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.
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 6 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

	UNL	1
  )
 (no restraints)
	Quit

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charmm:
0

Welcome to antechamber: molecular input file processor.

Info: Finished reading file (updated_alatis_output_compound_sdf.mol2).
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 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

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


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