Ondřej Schindler

Wow, this is really fast reaction! :) It should be standard serine. So, carbon (grey color) should have 2 hydrogens instead of 3. Moreover distance between carbon and hydrogen is...

OK, missing bonds are probably error of Avogadro. But unresolved problem is, that carbon of serine has 3 hydrogens instead of 2. You can see it even in your picture...

Any progress here, please?

And do you have any idea if you'll ever have time to do that? We are planning to use pdb2pqr for a large Alphafold2 related project and I don't know...

> This is not an extra atom -- its the alpha carbon hydrogen rotated the wrong way. There's a problem with the input structure that is affecting hydrogen optimization; e.g.,...

I am sending UniProt codes to 10 more problematic structures from AlphaFold DB. UniProt, pH, problematic atom index P56641, 12.3, 13 A0A1Z1CH22, 10.9, 23 Q3SAF8, 10.4, 405 J3QJY3, 13.7, 467...

[structures.zip](https://github.com/Electrostatics/pdb2pqr/files/11507882/structures.zip) There are 10 mentioned pqr files in the zip file. If you need to send more, let me know.

Hello, can I expect some progress, please? Should i send more structures with errors? I plan to use pdb2pqr in a publication on predicted structures I will write during the...

Any update on this, please?