[Chimera-users] Dock-preparation

[Eric Pettersen]

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 at 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
> <model1 (1).pdb>_______________________________________________
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