Use --whitespace for pdb2pqr #30
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Hi, thanks for your PR, this seems good to me. But let's wait for a comment from @vhoer. Best, |
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Hi, looks good to me, thank you! |
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Hi everyone,
When running
run_electrostatic, I have encountered couple of times problem with pqr conversion of my input pdb files.When running the
pdb2pqrwith default settings, for some atoms this conversion made the x,y,z fields merge.This is an example of such case:
11.992-150.282 -11.794where x and y merged. This made apbs fail with:Valist_readPQR: Error parsing atom 1! Please double check this atom in the pqr file, e.g., make sure there are no concatenated fields. Error reading molecules!In this PR I have added the
--whitespaceoption forpdb2pgrwhich fixes this problem by adding whitespaces between the fields.