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Cyclodextrin fixes #42

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merged 12 commits into from
Sep 27, 2019
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slochower
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This PR:

  • Fixes charges on MGLab 23 and MGLab 24. MGLab 23 was neutral and now it is -2; MGLab 24 was +1 and it is now neutral. @brandrade and I checked the pKa's with Marvin of all the side chains with Marvin. For MGLab 23, we determined that both carboxylates should be deprotonated. For MGLab 24, we also deprotonated the carboxylate (MGLab 24 is zwitterionic, and the existing protonation of the amine was correct.).
  • Accordingly, we updated the overview JPG and PDF files.
  • Also updates corresponding coded and noncoded CDX files.
  • Likewise, we updated the table of host charges in host_guest_description.md.
  • Deletes MGLab29 which does not correspond to anything.
  • Fixes a mixture of UNK and MGO residue names.
  • Eliminates all instances of atom name HQ which should correspond to a carbon. This has been mapped to atom name C9. This issue arose from the use MOE to build side chains from existing hydroxyls without changing the hydrogen atom name.
  • Reconnects missing bonds in the PDB section of several models.

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@davidlmobley davidlmobley left a comment

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Thanks, @slochower ! This looks good except that I'll update the main README.md to reflect these changes.

@davidlmobley
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Ah, this is from a fork, so I'll merge this first and THEN update the README.md.

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2 participants