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After minimizing a ligand (prepared with MarvinSketch) and preparing a target enzyme to dock said ligand onto (collected from RCSP PDB — 5DGN (Crystal structure of human FPPS in complex with compound 13)), I was met with an error

ValueError: Could not find atomic number for Hn Hn
cannot prepare ligand for AutoDock Vina; please look in Reply Log and/or run Chimera with --…

Reply Log

As a new user to the Chimera software, I neither knew what Hn Hn meant or how to troubleshoot this issue. I can also attach the mol files for the minimized ligand and prepared target enzyme if necessary to help with troubleshooting.

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    $\begingroup$ Not sure about Chimera specifically, but a google search for Hn turns up either 'Azanylidene' or maybe the old name for Hassium (Hs) which was "hahnium" (Hn)? $\endgroup$
    – gilleain
    Commented Jan 4, 2022 at 10:54
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    $\begingroup$ @Thunderbolt114 - It's not the PDB file, that's for sure. Can you do grep -A 5 -B 5 'Hn' minimized_file and report what it says? It's going to turn out to be something involving a missing hydrogen added to a nitrogen is my guess, but let's have a look. $\endgroup$ Commented Jan 4, 2022 at 22:44
  • $\begingroup$ Is that a command I input into the software? If so, how can I input it? I'm a bit confused. $\endgroup$
    – Mas
    Commented Jan 4, 2022 at 23:30
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    $\begingroup$ It's a command for a Linux or UNIX shell searching for Hn and printing five lines before and after. Pretty much like the search box in a Texteditor, just not worth the unnecessary graphical interface. $\endgroup$ Commented Jan 6, 2022 at 0:41
  • $\begingroup$ I'd also assume that questions like this have a bigger audience at Matter Modeling. Please be aware that cross posting is discouraged. $\endgroup$ Commented Jan 6, 2022 at 0:43

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I have the same error for thyroxine (T44.mol2). Definitely two hydrogens on the amine nitrogen. From the mol2 file:

     31 H6'        20.4230   40.7840   26.1950 H         1 T44    0.0000
     32 HN81       21.6870   45.6570   36.2000 H         1 T44    0.0000
     33 HN82       23.1470   46.0670   35.4150 H         1 T44    0.0000
     34 HO4'       22.9030   42.4090   22.4520 H         1 T44    0.0000

I presume these are the problem Hn Hn. Another mol2 file, triiodothyronine, has the same lines, but doesn't have the error!

The problem is definitely the hydrogens on the nitrogen. However, it is with the writing of the *.ligand.pdb file. If, as above, the original .mol2 (.pdb) file has HN81 and HN82 and HO4' all three will cause errors. The fix is the clean out the ligand's .mol2 (or .pdf) file and just have the element symbol in columns 9 and 10. Problem fixed. If the element name is 4 characters long, the software writes the "H" in the wrong column, 9 not 10 of the *.ligand.pdb file, to get space.

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  • $\begingroup$ Ahhh, what a wonderful, modern, flexible format .pdb is ... $\endgroup$
    – Ian Bush
    Commented Dec 8, 2023 at 5:41

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