Various PDB fixes

[IAlibay]

Fixes #68

TODO:

• Make sure HETATM are applied properly, and make sure Fix protein.pdb files; remove GROMACS-specific files; drop LFS usage #52 (comment) is fixed.
• Change the atom names for the caps to adhere to PDB naming conventions
• Remove ANISOU records for TYK2 and Thrombin
• Rename NMA caps to NME
• Don't have NME (or NMA) caps have icodes
• Rename first residue backbone hydrogen to correct naming scheme
• Make sure SSBOND entries are consistent - CONECT records for thrombin are there and it's all consistent with pdb4amber
• Fix pfkfb3 connection record
• Remove CONECT records for caps
• Work out what to do with TPO in cdk2 - double check CCD entry
• TNSK2, and PDE2 with bonded zinc and PDE2 with bonded magnesium?
  • Shift to LINKS

[IAlibay]

Note:

This doesn't necessarily fix things for AMBER, there are two cases where I expect failures with leap.

• Missing CYX residues in Thrombin: reasonably easily fixed with a pre-processing script like pdb4amber
• Incorrectly named protonated residues (e.g. HIP, HID, etc...): could be fixed by a template matching approach?

From a quick test at leap those seem to be the only issues for getting this working in AMBER.

[codecov]

Codecov Report

Merging #87 (4fef270) into main (e9b153e) will not change coverage.
The diff coverage is n/a.

Additional details and impacted files

[dotsdl]

@IAlibay will remove CONECT records for now; may re-add in 0.4.0

[dotsdl]

For structural ions, let's use LINKS entries to indicate their coordination.

[jchodera]

These changes look good to me!

I've confirmed the protein PDB files can all be read in OpenMM:

from openmm.app import PDBFile

from glob import glob
filenames = glob('data/*/01_*/crd/*.pdb')
print(filenames)

# Define the keyword arguments to feed to ForceField
from openmm import unit
from openmm import app
forcefield_kwargs = { 'constraints' : app.HBonds, 'rigidWater' : True, 'removeCMMotion' : False, 'hydrogenMass' : 4*unit.amu }
# Initialize a SystemGenerator using GAFF
from openmmforcefields.generators import SystemGenerator
system_generator = SystemGenerator(forcefields=['amber/ff14SB.xml', 'amber/phosaa14SB.xml', 'amber/tip3p_standard.xml'], small_molecule_forcefield='gaff-2.11', forcefield_kwargs=forcefield_kwargs, cache='db.json')

for filename in filenames:
    print(filename)
    pdbfile = app.PDBFile(filename)
    openmm_topology = pdbfile.topology
    # Create an OpenMM System from an OpenMM Topology object
    system = system_generator.create_system(openmm_topology)

[IAlibay]

Thanks for the review @jchodera !