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PDBFixer fixes problems in PDB files
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residue names based on protonation state? #172

Closed nitroamos closed 6 years ago

nitroamos commented 6 years ago

Is there any feature implemented whereby PDBFixer (or OpenMM) can name residues based on their protonation state? I'm interested in doing Amber and Gromacs calculations and I'm surveying approaches.

peastman commented 6 years ago

PDBFixer always produces standard PDB names for residues. Your best bet is probably to process the output file after it's done to rename the residues.

Does Amber really not provide tools to do this automatically? It's going to be an issue every time someone downloads a PDB file from RCSB and wants to simulate in with Amber.

nitroamos commented 6 years ago

I found the tool pdb4amber and it seems to work ok.