hydrogen atoms with zero radius ?!

[UnixJunkie]

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]

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.

[UnixJunkie]

Interesting; I did not know that. I think I used the amber FF.