Molfile to Params Conversion: LIG Molecule with Warnings and File Overwrite Issue

This is the output of a command-line program that converts a molecular file (molfile) to a parameter file (params). The input molecule is named 'LIG', and the output parameter file is also named 'LIG'. The molecule's conformers are stored in a separate file ('GRA_confs.sdf').

The output includes warnings and adjustments made to the molecule, such as:

• Duplicated atom names were detected and renamed.
• A warning about an atom ('S1') having a valence greater than 4.
• The molecule contains double bonds but no aromatic bonds, which might require explicit identification.
• The total naive charge (-6.315) was adjusted to the desired charge (-1.000) by offsetting all atoms by 0.111.

Further warnings about the molecule's characteristics were raised:

• Fragment 1 has a high number of atoms compared to typical protein residues.
• The number of non-hydrogen atoms in fragment 1 also exceeds the average for protein residues.
• Fragment 1 has a relatively high number of rotatable bonds.

The output also displays statistics about the molecule, such as:

• Average number of atoms and non-hydrogen atoms per fragment.
• A comparison with typical protein residues.

The program attempted to identify a root atom but failed and used the NBR atom instead.

Finally, the output indicates that the output file ('LIG.pdb' or 'LIG_conformers.pdb') already exists, preventing the program from overwriting it. To override the existing file, the '--clobber' option should be used.