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README
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README
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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)