Input:   /mnt/nfs/exa/work/elisfink/covalent_lib/nitriles/build_03282020/leads_elissa/try3_single/build_xaa/jobs/x/inputs/xadat
Working: n-1-101.cluster.ucsf.bkslab.org:/scratch/elisfink/99333/xadat-8131806.2048
Result:  /scratch/elisfink/99333/xadat-8131806.2048
Output:  /mnt/nfs/exa/work/elisfink/covalent_lib/nitriles/build_03282020/leads_elissa/try3_single/build_xaa/jobs/x/outputs/xadat
Task:    /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent --pre-tautomerized --permissive-taut-prot /mnt/nfs/exa/work/elisfink/covalent_lib/nitriles/build_03282020/leads_elissa/try3_single/build_xaa/jobs/x/inputs/xadat
mkdir: created directory `/scratch/elisfink/99333'
mkdir: created directory `/scratch/elisfink/99333/xadat-8131806.2048'
/scratch/elisfink/99333/xadat-8131806.2048 /mnt/nfs/exa/work/elisfink/covalent_lib/nitriles/build_03282020/leads_elissa/try3_single/build_xaa/jobs/x/logs
NOTICE: Using permissive tautomer and protomer thresholds. Could produce many protomers!
STORE_PROTOMERS is not set! Will keep all results to finished directory
mkdir: created directory `/scratch/elisfink/99333/xadat-8131806.2048/working'
mkdir: created directory `/scratch/elisfink/99333/xadat-8131806.2048/working/protonate'
Storing results in /scratch/elisfink/99333/xadat-8131806.2048/finished
Working in /scratch/elisfink/99333/xadat-8131806.2048/working
/scratch/elisfink/99333/xadat-8131806.2048/working /scratch/elisfink/99333/xadat-8131806.2048

/scratch/elisfink/99333/xadat-8131806.2048/working/protonate /scratch/elisfink/99333/xadat-8131806.2048/working /scratch/elisfink/99333/xadat-8131806.2048
Using inputs as protomers/tautomers. No processing done
1 substances and 1 protomers extracted
Coalesing and merging protomers
1 protomers generated for 1 compounds
Checking for new stereocenters and expanding
1 protomers after new stereo-center expansion
/scratch/elisfink/99333/xadat-8131806.2048/working /scratch/elisfink/99333/xadat-8131806.2048

Bulk generating 3D conformations all protomers in /scratch/elisfink/99333/xadat-8131806.2048/working/3D
mkdir: created directory `/scratch/elisfink/99333/xadat-8131806.2048/working/3D'
We are using corina for 3D embeding
debuging info:: /scratch/elisfink/99333/xadat-8131806.2048/working/protonate/xadat-protomers-expanded.ism /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh
removed `corina.trc'
2 3D conformations generated for 1 compounds

Building ZINC001332076190
mkdir: created directory `/scratch/elisfink/99333/xadat-8131806.2048/working/building'
mkdir: created directory `/scratch/elisfink/99333/xadat-8131806.2048/working/building/ZINC001332076190'
/scratch/elisfink/99333/xadat-8131806.2048/working/building/ZINC001332076190 /scratch/elisfink/99333/xadat-8131806.2048/working /scratch/elisfink/99333/xadat-8131806.2048
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for ZINC001332076190

mkdir: created directory `0'
/scratch/elisfink/99333/xadat-8131806.2048/working/building/ZINC001332076190/0 /scratch/elisfink/99333/xadat-8131806.2048/working/building/ZINC001332076190 /scratch/elisfink/99333/xadat-8131806.2048/working /scratch/elisfink/99333/xadat-8131806.2048
Protomer 0 (index: 1)
Found valid previously generated 3D confromation in /scratch/elisfink/99333/xadat-8131806.2048/working/3D/1
`/scratch/elisfink/99333/xadat-8131806.2048/working/3D/1' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N=C([SiH3])[CH]c1cccc(NC(=O)[C@]2(F)CCNC2)n1)

`ZINC001332076190.mol2' -> `0.mol2'
`temp.mol2' -> `ZINC001332076190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.