Hi Javad,
When Chimera assigns partial charges and atom types to standard residues, it simply looks up the name of the atom in a table. That means that the atoms in standard residues need to have their PDB standard names. The standard names for the hydrogens attached to CD1 in ILE residues are HD11, HD12, and HD13. In your structure those names are HD1, HD2, and HD3.
You need to correct your structure so that those atoms have their standard names. One way is for you to edit your file. Another way is to delete all the hydrogens in Chimera and let Chimera add them back, which will result in them having the standard names. You do that by opening he command line (Favorites→Command Line) and typing the command "del H". After that, your dock prep should work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

On Aug 17, 2020, at 5:12 AM, JAVAD KARIMBAYLI <javad.karimbayli01@universitadipavia.it> wrote:

Hi!
I have got a problem and searched all previous posts for solutions but failed to find one.
Therefore, I would be very much thankful to have your guidance.
I have generated my protein model in I-Tasser and now I would like to do dock-prep. 
 (Attached model-PDB file)
However, when I run it:
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
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