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Fix PDB files #68

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IAlibay opened this issue Oct 10, 2022 · 1 comment · Fixed by #87
Closed

Fix PDB files #68

IAlibay opened this issue Oct 10, 2022 · 1 comment · Fixed by #87
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Release 0.3.0

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IAlibay commented Oct 10, 2022 •
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Essentially #58 but this time directly against main.

Need to fix:

  • Make sure HETATM are applied properly, and make sure Fix protein.pdb files; remove GROMACS-specific files; drop LFS usage #52 (comment) is fixed.
  • Change the atom names for the caps to adhere to PDB naming conventions
  • Remove ANISOU records for TYK2 and Thrombin
  • Rename NMA caps to NME
  • Don't have NME (or NMA) caps have icodes
  • Make sure SSBOND entries are consistent (I believe this is already fine)
  • Assign correct hydrogen name for histidines (need to double check if this is PDB compliant)
@IAlibay IAlibay self-assigned this Oct 10, 2022
@IAlibay IAlibay added this to the Release 0.3.0 milestone Oct 10, 2022
@IAlibay IAlibay mentioned this issue Oct 11, 2022
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IAlibay commented Nov 28, 2022 •
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@ijpulidos I'm going to migrate that comment of yours re: POP in pfkfb3 here (#82 (comment)).

Seems like one we should have moved to a the cofactors sdf file. We should aim to deal with it alongside this once #82 is merged.

@IAlibay IAlibay mentioned this issue Jan 10, 2023
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IAlibay added a commit that referenced this issue Feb 7, 2023
@IAlibay
Various PDB fixes (#87)
d338760 
Fixes #68
* remove ANISOU records
* HETATM caps, remove NMA icodes
* NMA to NME, fix cap hydrogen names
* Remove cap CONECT records
* fix hydrogen naming for ace bonded terminal AAs
* move pde2 ion connections to LINK section
* move ion coordination bonds to LINK section
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Various PDB fixes openforcefield/protein-ligand-benchmark
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@dotsdl @IAlibay