v4-0h08-0

command from alatis:
	antechamber -at gaff2 -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:
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
-- Check Unusual Elements --
Warning: Unusual element (Si) for atom (ID: 13, Name: Si13).
Warning: Unusual element (Si) for atom (ID: 14, Name: Si14).
Warning: Unusual element (Si) for atom (ID: 15, Name: Si15).
Warning: Unusual element (Si) for atom (ID: 16, Name: Si16).
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: /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 gaff2
Info: Total number of electrons: 160; 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:
139
Warning: Atom type (Si) is not in PARMCHK.DAT; using default values
         for improper_flag [0], group_id [0], and equivalent_flag [0].
Warning: No mass information for atom type (Si); set to 0.0.
         It is recommended to add the new atom type (Si) to PARMCHK.DAT.
Segmentation fault (core dumped)

<***************>
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.gaff2
----- Source of /usr/software/amber16/dat/leap/cmd/leaprc.gaff2 done
Log file: ./leap.log
Loading parameters: /usr/software/amber16/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.1, April 2016)
Loading Mol2 file: ./updated_alatis_output_compound_3D_h_sdf.mol2
Reading MOLECULE named UNL
Checking 'updated_alatis_output_compound_3D_h_sdf'....
Checking parameters for unit 'updated_alatis_output_compound_3D_h_sdf'.
Checking for bond parameters.
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Checking for angle parameters.
Could not find angle parameter: c3 - Si - c3
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - c3
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - c3
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - c3
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: os - Si - os
Could not find angle parameter: os - Si - os
Could not find angle parameter: os - Si - os
Could not find angle parameter: os - Si - os
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - os - Si
Could not find angle parameter: Si - os - Si
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - os - Si
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - os - Si
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
There are missing parameters.
Unit is OK.
Loading parameters: ./updated_alatis_output_compound_3D_h_sdf.frcmod
Reading title:
Checking 'updated_alatis_output_compound_3D_h_sdf'....
Checking parameters for unit 'updated_alatis_output_compound_3D_h_sdf'.
Checking for bond parameters.
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: c3 - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Could not find bond parameter for: os - Si
Checking for angle parameters.
Could not find angle parameter: c3 - Si - c3
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - c3
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - c3
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - c3
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: c3 - Si - os
Could not find angle parameter: os - Si - os
Could not find angle parameter: os - Si - os
Could not find angle parameter: os - Si - os
Could not find angle parameter: os - Si - os
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - os - Si
Could not find angle parameter: Si - os - Si
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - os - Si
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - os - Si
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
Could not find angle parameter: Si - c3 - hc
There are missing parameters.
Unit is OK.
 Creating updated_alatis_output_compound_3D_h_sdf.lib
Building topology.
Building atom parameters.
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<UNL 1>.A<Si13 13> Could not find vdW (or other) parameters for type: Si
For atom: .R<UNL 1>.A<Si14 14> Could not find vdW (or other) parameters for type: Si
For atom: .R<UNL 1>.A<Si15 15> Could not find vdW (or other) parameters for type: Si
For atom: .R<UNL 1>.A<Si16 16> Could not find vdW (or other) parameters for type: Si
Parameter file was not saved.
	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_3D_h_sdf.mol2).
-- Check Unusual Elements --
Warning: Unusual element (Si) for atom (ID: 13, Name: Si13).
Warning: Unusual element (Si) for atom (ID: 14, Name: Si14).
Warning: Unusual element (Si) for atom (ID: 15, Name: Si15).
Warning: Unusual element (Si) for atom (ID: 16, Name: Si16).
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: /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 gaff2

Running: /usr/software/amber16/bin/atomtype -i ANTECHAMBER_PREP.AC0 -o ANTECHAMBER_PREP.AC -p gaff2

Running: /usr/software/amber16/bin/charmmgen -i ANTECHAMBER_PREP.AC -f ac -o updated_alatis_output_compound_3D_h_sdf.charmm -r MOL


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