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jensengroup / propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
http://propka.org
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Missing atoms or failed protonation #147

Closed rediaz111 closed 11 months ago

rediaz111 commented 2 years ago

When I try to run propka 3 filename.pdb -o pH -d, I receive the following error.

Missing atoms or failed protonation for TRP 301 A (BBN) -- please check the structure Group (BBN) for 4854- N 301-TRP (A) [ -1.008 0.307 -13.092] N Expected 2 interaction atoms for acids, found: 0- H1 301-TRP (A) [ -0.834 -0.673 -12.919] H 0- H2 301-TRP (A) [ -0.814 0.517 -14.061] H 4854- N 301-TRP (A) [ -1.008 0.307 -13.092] N Expected 2 interaction atoms for bases, found: 0- H1 301-TRP (A) [ -0.834 -0.673 -12.919] H 0- H2 301-TRP (A) [ -0.814 0.517 -14.061] H 4854- N 301-TRP (A) [ -1.008 0.307 -13.092] N Missing atoms or failed protonation for TRP 348 A (BBN) -- please check the structure Group (BBN) for 5653- N 348-TRP (A) [ -4.353 18.104 -29.876] N Expected 2 interaction atoms for acids, found: 0- H1 348-TRP (A) [ -3.859 17.366 -29.395] H 0- H2 348-TRP (A) [ -4.843 18.675 -29.203] H 5653- N 348-TRP (A) [ -4.353 18.104 -29.876] N Expected 2 interaction atoms for bases, found: 0- H1 348-TRP (A) [ -3.859 17.366 -29.395] H 0- H2 348-TRP (A) [ -4.843 18.675 -29.203] H 5653- N 348-TRP (A) [ -4.353 18.104 -29.876] N Missing atoms or failed protonation for TRP 301 A (BBN) -- please check the structure Group (BBN) for 4854- N 301-TRP (A) [ -1.008 0.307 -13.092] N Expected 2 interaction atoms for acids, found: 0- H1 301-TRP (A) [ -0.834 -0.673 -12.919] H 0- H2 301-TRP (A) [ -0.814 0.517 -14.061] H 4854- N 301-TRP (A) [ -1.008 0.307 -13.092] N Expected 2 interaction atoms for bases, found: 0- H1 301-TRP (A) [ -0.834 -0.673 -12.919] H 0- H2 301-TRP (A) [ -0.814 0.517 -14.061] H 4854- N 301-TRP (A) [ -1.008 0.307 -13.092] N Missing atoms or failed protonation for TRP 348 A (BBN) -- please check the structure Group (BBN) for 5653- N 348-TRP (A) [ -4.353 18.104 -29.876] N Expected 2 interaction atoms for acids, found: 0- H1 348-TRP (A) [ -3.859 17.366 -29.395] H 0- H2 348-TRP (A) [ -4.843 18.675 -29.203] H 5653- N 348-TRP (A) [ -4.353 18.104 -29.876] N Expected 2 interaction atoms for bases, found: 0- H1 348-TRP (A) [ -3.859 17.366 -29.395] H 0- H2 348-TRP (A) [ -4.843 18.675 -29.203] H 5653- N 348-TRP (A) [ -4.353 18.104 -29.876] N

I'm not sure how to fix this issue. Apo_refine_50_Up.txt

rediaz111 commented 2 years ago

I wanted to follow up on this error that I'm receiving. I don't see anything in the PDB file that points toward what the issue is.

Loci-Tran commented 11 months ago

@rediaz111 I am getting the same problem with you. No answer -_- Have you fixed it or know the reasons?

It seems for the whole structure propka only predicts most of them, but not all.

sobolevnrm commented 11 months ago

Do either of you have a PDB entry that reproduces the results? The attachment about looks like a custom PDB file.

Thanks.

rediaz111 commented 11 months ago

PDB ID: 8fg5

speleo3 commented 11 months ago 
propka3 8fg5.pdb -o 7.0 -d

Runs without errors or warnings for me, using propka 3.5 or 3.4 (with older versions I get an AttributeError).

The attached Apo_refine_50_Up.txt has two residues (300 and 347) with Alt code B but no A. If I change those to A, the errors go away.