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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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hydrogen atoms with zero radius ?! #346

Closed UnixJunkie closed 1 year ago

UnixJunkie commented 1 year ago

Hello,

While processing PDB:3RFM, I noticed that in the output .pqr file, some Hs have a radius of 0.0000. Why? Should I be worried (I already am, honestly)?

I used https://server.poissonboltzmann.org/pdb2pqr but also pdb2pqr (Version 2.1.1) from the command line.

Thanks a lot, Francois.

sobolevnrm commented 1 year ago

Some force fields (e.g., PARSE) use zero-radius parameters for some atoms, particularly hydrogen in some environments. This generally occurs when the radius of the heavy atom is large enough to encompass the entirety of the hydrogen atom, eliminating the need for a non-zero hydrogen radius.