PDB files for BRD4 parameterized systems are missing CONECT records

[jchodera]

The BRD4-*.pdb files in this directory are missing the required CONECT records for the small molecule ligands.

As a result:

1. They are not even valid PDB files, which require CONECT records for nonstandard residues
2. They cannot be used to build parameterized molecular systems

[davidlmobley]

I believe these are from @GHeinzelmann who, I believe, used these with AMBER to set up his systems.

I realize the PDB format requires CONECT entries as part of the specification, but as you're well aware, not every toolkit conforms to the specs.

[jchodera]

It looks like ambpdb -p BRD4-1.prmtop -c BRD4-1.crds -conect > BRD4-1.pdb will create the PDB file with the correct CONECT records. I'll do this now and open a PR.