Tools .. Strct edit .. Dockprep
All selected 
 Add hydrogens (also consider H-bonds)

Incomplete side chains:replace(Dunbrack 2010 rotamer library)

Protonation states fro: his (residue-name-based)

standart residues: AMBER ff14SB

other residues: AM1-BCC

Output:

No incomplete side chains
No SEQRES records for model1 (1).pdb (#0) chain A; guessing terminii instead
Chain-initial residues that are actual N terminii: MET 1.A
Chain-initial residues that are not actual N terminii: 
Chain-final residues that are actual C terminii: 
Chain-final residues that are not actual C terminii: LEU 522.A
470 hydrogen bonds
Removing spurious proton from 'C' of LEU 522.A
Hydrogens added
Charge model: AMBER ff14SB
Non-standard atom names:
	ILE HD3 (ILE 18.A HD3, ILE 31.A HD3, ILE 42.A HD3 + 26 others)
	ILE HD1 (ILE 18.A HD1, ILE 31.A HD1, ILE 42.A HD1 + 26 others)
	ILE HD2 (ILE 18.A HD2, ILE 31.A HD2, ILE 42.A HD2 + 26 others)
Total charge for #0: 9.382
The following residues had non-integral charges:
	ILE 18.A -0.0558
	ILE 31.A -0.0558
	ILE 42.A -0.0558
	ILE 77.A -0.0558
	ILE 96.A -0.0558
	ILE 132.A -0.0558
	ILE 136.A -0.0558
	ILE 151.A -0.0558
	ILE 153.A -0.0558
	ILE 163.A -0.0558
	ILE 184.A -0.0558
	ILE 193.A -0.0558
	ILE 223.A -0.0558
	ILE 236.A -0.0558
	ILE 250.A -0.0558
	ILE 256.A -0.0558
	ILE 284.A -0.0558
	ILE 297.A -0.0558
	ILE 321.A -0.0558
	ILE 370.A -0.0558
	ILE 378.A -0.0558
	ILE 401.A -0.0558
	ILE 416.A -0.0558
	ILE 436.A -0.0558
	ILE 447.A -0.0558
	ILE 450.A -0.0558
	ILE 480.A -0.0558
	ILE 489.A -0.0558
	ILE 495.A -0.0558
Correct charges are unknown for 3 non-standard atom names in otherwise standard residues

Charges of 0.0 were assigned to the unknown atoms

So, please kindly help me to solve the issue.

Yours Sincerely

Javad Karimbayli