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