water hydrogen element error

Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

http://www.poissonboltzmann.org/

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water hydrogen element error #193

Closed dongdawn closed 2 years ago

dongdawn commented 3 years ago

After adding hydrogen in O, the element O was assigned, however, it should be H.

sobolevnrm commented 3 years ago

Hello -- this definitely looks like a bug. Thank you for letting us know!

stefdoerr commented 3 years ago

Hi, this is caused by the create_atom function not setting the element and copying the element of the reference atom of the water which is an oxygen. It's fixed in this PR https://github.com/Electrostatics/pdb2pqr/pull/195

sobolevnrm commented 2 years ago

@stefdoerr claims this has been fixed and I can't reproduce the original error so I am closing the issue.