I convert my pdb to charmm and get hydrogens removed

[Vytas Vytautas]

Here I attach my pdb file it is heavily based on protein data bank 1r5s just hydrogens are added and the first conformation is retained with ChimeraX. Then I try to do:

pdb <- read.pdb("1r5s_11.pdb")
new <- convert.pdb(pdb, type="charmm")
Retaining 997 non-hydrogen atoms
Removing a total of 938 atoms
Converting to 'charmm' format
Found 0 possible chain breaks
write.pdb(new, file="1r5s_11_charmm.pdb")

packageVersion("bio3d")
[1] ‘2.4.4’

And get all my hydrogens removed. R 4.2.2. The same happens with another pdb file I tried.

[Xinqiu Yao]

You need to set rm.h=FALSE. By default, it is TRUE and will remove hydrogens.