Description
I am trying to re-create those pre-processed data. I am encountering 2 problems for creating protein's gninatypes files.
- Remove water and hydrogen from XXX_protein.pdb to generate XXX_nowat.pdb. I only retain those lines beginning with "ATOM" except for hydrogen by my own code. However, sometimes my results are a bit different with XXX_nowat.pdb in the downloaded datasets. I notice some of the XXX_nowat.pdb in datasets cut the protein chains "B" compared with the original protein PDB file if the protein has more than 2 chains, but not always. Is there a script to create XXX_nowat.pdb to share with me ?
2）Create XXX_rec_0.gninatypes. Even though I am using the ready-made XXX_nowat.pdb file to create gninatypes files by "gninatyper". The files generated by my gninatyper are also different with the existing XXX_rec_0.gninatypes. I compared the 2 result files and find the atoms coordinate are actually right, but some atoms' types are different . E.g. the "NitrogenXSDonor" in the ready-made file is labeled as "NitrogenXSAcceptor" in my result, and "AromaticCarbonXSHydrophobe" is labeled as "AliphaticCarbonXSHydrophobe". Is it caused by my gnina version , "master:e60ccc0+", newer than the ready-made gninatypes files ?
Thanks a lot !