failed steps in receptor preparation; documentation on receptor prep? about waterkit

[jeeberhardt]

Thanks for the feedback!

For the first issue, it might be related to the hydrogen atoms. What happens if you add the --keep_hydrogen argument to the command line? (Also I already see a stupid bug that I would need to fix once I have access to a computer..)

For the second issue, isn't it related to the space between pd and b in the input pdb filename?

For the third and last issue, if you add a TER record between the protein and the following ligand, and between each ligand after you should not have this issue anymore. FYI, the script is expecting the input to (kind of) follow the specification of the PDB format, so the end of a chain (ATOM/HETATM) must be specified by a TER record. Otherwise it is a bit hard to know if a gap observed between two residues is « normal » or not.

[blakemertz]

@jeeberhardt thanks for the quick response -- apologies for not replying sooner.

I needed to start digging through my pdb files to get them to process correctly in waterkit. Thank you for catching the improper file extension on that pdb in my 2nd issue.

The first issue I'm not sure will get resolved anytime soon -- there is something a little funky in how Maestro is exporting files into pdb format that ambertools doesn't handle properly, so for now I will just stick with the PyMOL workaround. I was able to resolve the 3rd issue with my pdb that was exported in PyMOL. Maestro was inserting "A---" in columns 73-76 for a noticeable fraction of my atom entries for some reason. To get around that, I had to do the following:

1. Export to pdb in Maestro
2. Remove the "A---" from all ATOM entries
3. Load into PyMOL and export to pdb.

I'll mark this closed, will pick this up again if I get some fresh ideas on why Maestro is introducing that funk in the pdb file.