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#286 incorrect H adding: need physiological protonation phmodel

2.2.x
closed
Tim Vandermeersch
Library Functions (223)
5
2012-10-23
2007-08-24
Felix_P
No

I would like to report a problem with openbabels function of adding hydrogens to proteins. I used three different versions and hydrogens were added in three different ways.

my home open babel (GUI on windows XP, I don't find the version number anywhere) does not recognise double bonds in the protein file and adds to many hydrogens, e.g. in His. Using the pH model will do the correct task (making ammonium and carboxylic ions) only that it is wrong because the bond order was neglected.

at work I used a different openbabel (command line on Linux, I am afraid I don't know the version either). it recognised the bonds correctly but it protonated His which is not protonated (neutral, one N and one N-H) in physiological conditions. Arg was correctly protonated

a different babel version kept both Arg and His unprotonated which is wrong again.

I am sorry that I could not give more specific information but maybe I could point out that there still seems to be a problem with protonation.

A solution may be to save the physiological protonation of the amino acids in phmodel.txt

Thanks for making such a nice program available.

Best regards

Felix

Discussion

  • Chris Morley

    Chris Morley - 2007-08-24

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    Thanks for the report.

    Most of the code in OpenBabel is the same whatever the platform. This includes that for hydrogen addition, but, as you point out, it may use data in some .txt files. If these are not present, as in the Windows distribution, an internal set of data are used, which should be the same as in the default .txt files, unless something has gone wrong.

    It would be helpful if you could attach an example file, and try to find the version numbers:
    menu item Help/About on the Windows GUI and babel -V on the commandline.

    Chris

     

  • Felix_P

    Felix_P - 2007-08-26

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    I did not find a menu in my OpenBabel windows GUI. maybe my version is too old. the DOS prompt tells me it's "Open Babel 2.0.0 -- Dec 1 2005 -- 13:55:06"

    I don't know the versions I had at my summer project

    I could not upload the file because it is bigger than the maximum allowed: the file can be found at http://www.rcsb.org/pdb/files/1g50.pdb
    residues to look at are for example: Arg335 - both terminal nitrogens should be protonated (the residue is charged +); and His356 - only one ring nitrogen is protonated (the residue is neutral)

    Thanks

    Felix

     

  • Geoff Hutchison

    Geoff Hutchison - 2008-06-04

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    Tim could you look at this? I think the suggestion is a good one -- provide physiological protonation for the amino acids into phmodel.txt

    If you need suggestions about how to use phmodel, please let me know.

     

  • Geoff Hutchison

    Geoff Hutchison - 2008-06-10

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    I believe Tim's recent changes to SVN trunk solve this -- the pH model will now recognize the separate pKas of each amino acid and will adjust accordingly.

     

  • SourceForge Robot

    SourceForge Robot - 2008-06-25

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    This Tracker item was closed automatically by the system. It was
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    did not respond within 14 days (the time period specified by
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