[Chimera-users] Dock-preparation

[JAVAD KARIMBAYLI]

Thanks a lot dear Eric for your prompt reply.
Much appreciated!
Javad Karimbayli

On Mon, 17 Aug 2020 at 17:20, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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
>
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