problem of renamed atoms in running molfile_to_params.py

Hi all,

I am running molfile_to_params.py for my ligand to get the .params file, but the .params file generated by this script is not matched with .mol2 file that I use. This script changes the name of atoms and gives me a new pdb file in which name of atoms are different from my original .mol2 file. Moreover, I get a warning when running this code (which is copied below).  It is noteworthy to mention that all atom names in my ligand are unique.

I need a .params file which are matched with my original pdb file.

I would be grateful,if you could help me.

Atom names contain duplications — renaming all atoms.

WARNING:  structure contains double bonds but no aromatic bonds

  Aromatic bonds must be identified explicitly —

  alternating single/double bonds (Kekule structure) won’t cut it.

  This warning does not apply to you if your molecule really isn’t aromatic.

Total naive charge -4.835, desired charge 0.000, offsetting all atoms by 0.056

WARNING: fragment 1 has 87 total atoms including H; protein residues have 7 – 24 (DNA: 33)

WARNING: fragment 1 has 40 non-H atoms; protein residues have 4 – 14 (DNA: 22)

WARNING: fragment 1 has 30 rotatable bonds; protein residues have 0 – 4

Average 87.0 atoms (40.0 non-H atoms) per fragment

(Proteins average 15.5 atoms (7.8 non-H atoms) per residue)

WARNING:  no root atom specified, using auto-selected NBR atom instead.

Wrote params file XYZ.params

Wrote PDB file XYZ_0001.pdb