Outputs miss some hydrogen atoms in protein

HADDOCK
1

It looks like standalone HADDOCK outputs only some hydrogen atoms in protein, the one near the polar groups. This happens even though all hydrogen atoms were present in the input files. This is then an issue when one would like to follow up with some MD calculations where all hydrogen atoms must be present.

Is there a way to make HADDOCK outputting all hydrogen atoms as they were present in the input pdbs?

Thanks.

2

The parameter you are looking for is delenph, in the run.cns file

{* Remove non-polar hydrogens? *}
{+ choice: true false +}
{===>} delenph=true;
3

Thank you @honoratorv!

4

But it will take more CPU time to keep all non-polar hydrogens.

Simple to add them after HADDOCK, e.g. with hbplus or reduce