chianina.nmrfam.wisc.edu

command from alatis:
	/opt/amber16/bin/antechamber -i updated_alatis_output_bmse000687_mol.pdb -fi pdb -o  updated_alatis_output_bmse000687_mol.mol2 -fo mol2 -c bcc -s 2
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: /opt/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 ALA ---

---Judge bond type for Residue 2 with ID of 0 and Name of UNK ---

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

---Judge bond type for Residue 4 with ID of 0 and Name of UNK ---

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

---Judge bond type for Residue 6 with ID of 0 and Name of UNK ---

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

---Judge bond type for Residue 8 with ID of 0 and Name of UNK ---

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

---Judge bond type for Residue 10 with ID of 0 and Name of UNK ---

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

---Judge bond type for Residue 12 with ID of 0 and Name of UNK ---

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

Running: /opt/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 130; net charge: 0

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

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

Running: /opt/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 /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)
Loading Mol2 file: ./updated_alatis_output_bmse000687_mol.mol2
Reading MOLECULE named ALA
Checking 'updated_alatis_output_bmse000687_mol'....
Checking parameters for unit 'updated_alatis_output_bmse000687_mol'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Loading parameters: ./updated_alatis_output_bmse000687_mol.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Checking 'updated_alatis_output_bmse000687_mol'....
Checking parameters for unit 'updated_alatis_output_bmse000687_mol'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
 Creating updated_alatis_output_bmse000687_mol.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 12 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

	ALA	1
  )
 (no restraints)
	Quit

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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_bmse000687_mol.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: /opt/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 ALA ---

---Judge bond type for Residue 2 with ID of 0 and Name of UNK ---

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

---Judge bond type for Residue 4 with ID of 0 and Name of UNK ---

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

---Judge bond type for Residue 6 with ID of 0 and Name of UNK ---

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

---Judge bond type for Residue 8 with ID of 0 and Name of UNK ---

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

---Judge bond type for Residue 10 with ID of 0 and Name of UNK ---

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

---Judge bond type for Residue 12 with ID of 0 and Name of UNK ---

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

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

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

Running: /opt/amber16/bin/charmmgen -i ANTECHAMBER_PREP.AC -f ac -o updated_alatis_output_bmse000687_mol.charmm -r MOL


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