Add DNA atoms to forcefield if possible

[rgayatri]

Following are the warnings when encountered with DNA chains in PDBs

WARNING: not mentioned in top or patch: ('DC', 'C5')
WARNING: not mentioned in top or patch: ('DC', 'C5')
WARNING: not mentioned in top or patch: ('DC', 'C6')
WARNING: not mentioned in top or patch: ('DC', 'C6')
WARNING: not mentioned in top or patch: ('DC', 'P')
WARNING: not mentioned in top or patch: ('DC', 'P')
WARNING: not mentioned in top or patch: ('DC', 'OP1')
WARNING: not mentioned in top or patch: ('DC', 'OP1')
WARNING: not mentioned in top or patch: ('DC', 'OP2')
WARNING: not mentioned in top or patch: ('DC', 'OP2')
WARNING: not mentioned in top or patch: ('DC', "O5'")
WARNING: not mentioned in top or patch: ('DC', "O5'")

The PDBs with DNA are removed from hdf5 file due to errors in computing forcefield params.

ERROR: Error while computing deeprank.features.variant_conservation for 2YPA:B:589:Leucine->Valine: Traceback (most recent call last):
  File "/home/gayatrir/Work/DeepRank/DeepRank-Mut/deeprank/generate/DataGenerator.py", line 1456, in _compute_features
    feat_module.__compute_feature__(environment, distance_cutoff, featgrp, variant)
  File "/home/gayatrir/Work/DeepRank/DeepRank-Mut/deeprank/features/variant_conservation.py", line 51, in __compute_feature__
    residue_row = conservations_dataframe.iloc[variant.protein_residue_number - 1]
  File "/home/gayatrir/anaconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 895, in __getitem__
    return self._getitem_axis(maybe_callable, axis=axis)
  File "/home/gayatrir/anaconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 1501, in _getitem_axis
    self._validate_integer(key, axis)
  File "/home/gayatrir/anaconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 1444, in _validate_integer
    raise IndexError("single positional indexer is out-of-bounds")
IndexError: single positional indexer is out-of-bounds

For protein-DNA complexes, polar contacts and electrostatic interactions play a key role. It might be useful to include these in the training set.