[Chimera-users] Non-standard atom names

[Francesco Pietra]

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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