FILELIST
ene_final_min.dat - list of final energies from no solvent minimization
ene_initial_min.dat - list of inital ene from no solvent min
ene_final_min_igb.dat - list of final energies from GB minimization
ene_initial_min_igb.dat - list of initial ene from GB min
AmberDirectory - list of all components, NOT UP TO DATE
missing_mol2.dat - list of components antechamber failed
missing_min_pdb.dat - list of components sander minimization failed
outliers_min_energy.dat - no solvent minimization outliers (gradient RMSD >1000 or |energy|>1000)
outliers_min_igb_energy.dat - GB minimization outliers (gradient RMSD >1000 or |energy|>1000)

1. Procedure
To create AmberLibrary, run source/master_run.sh on the CCI computers. This essentially runs four scripts:
	elbow.generate_all_chemical_component_restraint_files.py (a copy of which is in source)
	run_tleap_sander.py
	run_mogul.py
	run_validation.py

What generate_all_chemical_component_restraint_files.py does:
run -> run_ligand_loop -> get_amber_filenames_from_directory_tree -> calculate_amber_files

Components of the "calculate_amber_files" routine:
  builder.run
  mol.OptimiseHydrogens
  mol.WritePDB ->4antechamber.pdb/final.pdb
  mol.Multiplicitise
  antechamber first run (charge/multiplicity from elbow, bcc, gaff) ->sqm.pdb
  antechamber second run (now using the sqm optimized geometry structure from the first run) ->mol2
  parmchk2 (make frcmod file) ->frcmod

FAQ
- What does builder.run do? elbow gets pdb ideal geometry - better for amber to start, matrix of bonds angles, chirals, protonation (based on 7.0 pH); deprotonates carboxylate, sulfate, protonates amine
- What is OptimiseHydrogens do? optimizes 
- What does Multiplicitise do? get multiplicity

Creates two sets - with H and without. Neutron diffraction where not deprotonated.


2. Quantity
[pjanowsk@krakow AmberLibrary]$ ./get_AmberLib_statistics.py 
Total no of *.final.pdb files (made by eLBOW): 14560
Total no of *.mol2 files (made by antechamber): 13627
Total no of *.mol2 files (made by prmchk2): 13627
Total no of *.min.pdb files (made by sander): 13310
Total no of *.min_igb.pdb files (made by sander): 13526

~19000 in components.cif
??? non-polymers 
~1500 failed eLBOW - no metals, too long smiles
14560 final.pdbs
13627 mol2   (933 failed antechamber)
13310 min.pdb  (317 failed sander)
13526 min_igb.pdb (101 failed sander igb)
13221 good minimizations (89 outliers) (outlier is RMSD >1000 or |energy|>1000
13467 good igb minimizations (59 outliers)



3. Causes of minimization failure:
I. failed no solvent but did not fail igb
  a.  Ewald PARAMETER RANGE CHECKING:
      parameter a: (unit cell size)  has value  0.15778E+04
      This is outside the legal range
      Lower limit:  0.10000E+01 Upper limit:  0.10000E+04
      Check ew_legal.h                                                 76  (high coordinates in mol2 file)
  b.  Frac coord min, max: -4.7028288463886145 3.0768178613122550
      The system has extended beyond
       the extent of the virtual box.
      Restarting sander will recalculate
       a new virtual box with 30 Angstroms
       extra on each side, if there is a
       restart file for this configuration.
      SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
      Atom out of bounds. If a restart has been written,
       restarting should resolve the error                             131 
  c. PARAMETER RANGE CHECKING:
      parameter nfft1: (grid size)  has value     2304
      This is outside the legal range
      Lower limit:        6 Upper limit:     2048
      The limits may be adjustable; search in the .h files             8 (high coords and molecule broke apart)
  d.  compute_nfft: failed to get good fft array size  
      x =    1627.7719999999999                                        1  (high coordinates)
II. failed both no solvent and igb
  a. I could not understand line     3 :
     -604.6010000-1939.4590000-756.2940000-603.9620000-1940.0720000-757.3010000  98  (high coords and molecule broke apart)
  b. Error opening unit    9: File "169.rst7" is missing or unreadable            3  (W2R and C4A are empty from eLBOW, 169 has high coords and broke apart)


4. Quality validation...
 ? bad energies
 ? bond/angle rmsd 
 ? mogul


W2R/C4A (empty final.pdb)