[Chimera-users] Non-standard atom names

[Eric Pettersen]

Hi Francesco,
	To identity the zero-charge atoms you should look in the Reply Log  
(under Favorites) -- it will list them explicitly.
	I guess I don't understand how you're getting these uncharged  
hydrogens given the procedure you outlined.  The hydrogens listed  
definitely aren't ones you would expect in those residues.  Typically  
the only way that happens is if there are residues with incomplete  
side chains that then get protonated -- the protons go into positions  
that "should" have heavy atoms and get names that don't correspond to  
normal proton names for that residues (since they aren't normal  
protons for that residue).  But with your procedure that should not  
have happened.  Are you sure that you didn't uncheck the "Mutate  
residues with incomplete side chains" step?  That step removes  
incomplete side chains and should prevent this kind of charge problem.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu


On Oct 16, 2007, at 8:06 AM, Francesco Pietra wrote:

> Problems with atom names in preparing a protein for docking. The  
> protein (K ion
> channel) was obtained as monomer from Protein Data Bank and then as  
> tetramer
> from Protein Quaternary Structure database through Chimera Fetch  
> ID. The
> tetramer was stripped to leave
>
> --Two helices
> --Selectivity filter
> --Pore helix
>
> Prepare with Chimera 1.2422 (I had previously carried out  
> successfully the
> tutorial) along defaults
>
> Tools .. Strct edit .. Dockprep
> All selected except "Delete non-complexed ions"
> Add hydrogens (also consider H-bonds)
>
> To write mol2 use untrasnformed coordinates; use Sybyl type H  
> naming; write
> current selection to @SETS, Save
>
> reported:
> Correct charges are unknown for 15 non-standard atom names in  
> otherwise
> standard residues (charges 0.0 assigned to these atoms.
> 1 model had non integral total charge.
>
> Looking at the mol2 file, I could only identify nine type of atoms  
> assiggen
> 0.0000 charge:
>
> H, HD1, HD2, HE1, HE2, HG1, HG2, HH1, HH2
>
> such as (for a small initial portion):
>
> 2 H .... 1 SER1
> 50 HD1 ... 4 LEU4
> 95 HD1 .... 7 LEU7
> 97 HD2 ... 7 LEU7
> 135 HG2 ... 10 THR10
> 150 HD1 ..... 11 LEU11
> 168 HE2 .... 12 GLN12
> 226 HH1 ... 16 ARG16
> 259 HD2 ... 18 LEU18
> 279 HD1 ... 20 LEU20
> 281 HD2 .. 20 LEU20
> 294 HD1 ... 21 LEU21
> 296 HD2 ... 21 LEU21
> 306 HG2 ... 22 ILE22
> 308 HG1 ... 22 ILE22
> 310 HD1 ... 22 ILE22
> 365 HD2 ... 25 LEU25
> 397 HG1 ... 27 ILE27
> 430 HG1 .. 30 ILE30
> 445 HD1 ... 31 LEU31
> 578 HE1 ... 40 GLU40
> 601 HD1 ... 42 ASP42
> 718 HG2 ... 51 ILE51
> 847 HG1 ... 59 VAL59
> 861 HG2 ... 60 VAL60
> 900 HG2 ... 63 THR63
> 926 HG2 ... 65 VAL65
> 974 HD1 ... 69 ASP69
> 1037 HG2 ... 73 ILE73
> 1039 HG1 ... 73 ILE73
> 1041 HD1 ... 73 ILE73
> 1063 HG1 ... 75 VAL75
>
> Being new to these procedures, could you please indicate how to fix  
> the issue?
>
> Thanks
>
> francesco pietra
>
>
>
>
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