# Janssen Ligand tutorial: why no -H2Hpolar flag in atoms\_to\_morph.py?

**URL:** <https://ask.bioexcel.eu/t/janssen-ligand-tutorial-why-no-h2hpolar-flag-in-atoms-to-morph-py/4210>\
**Category:** pmx\
**Created:** [March 22, 2023, 8:40am UTC](https://ask.bioexcel.eu/t/janssen-ligand-tutorial-why-no-h2hpolar-flag-in-atoms-to-morph-py/4210 "2023-03-22T08:40:45Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![obeyens](https://avatars.discourse-cdn.com/v4/letter/o/c77e96/32.png) [@obeyens](https://ask.bioexcel.eu/u/obeyens)\
**Post date:** [March 22, 2023, 8:40am UTC](https://ask.bioexcel.eu/t/janssen-ligand-tutorial-why-no-h2hpolar-flag-in-atoms-to-morph-py/4210/1 "2023-03-22T08:40:45Z")

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Dear all,

I am doing the Janssen ligand tutorial: [Ligand modification free energy calculations](http://pmx.mpibpc.mpg.de/janssen_tutorial_ligand/index.html#contents). During the atom mapping step using atoms\_to\_morph.py the following command is used:

$ python atoms\_to\_morph.py -i1 lig\_1a/lig\_1a.pdb -i2 lig\_5/lig\_5.pdb -o pairs.dat -alignment -H2H

I however noticed that this command introduces dummy hydrogens also on the nitrogens by not pairing the polar hydrogens. Upon testing a few flags for the atoms\_to\_morph.py script, I found that these polar hydrogen dummy atoms can be removed using the -H2Hpolar flag for the atoms\_to\_morph.py script. Why does the tutorial propose to add dummy atoms for polar hydrogens? Is there a specific reason for this?

Thank you in advance!

Kind regards,

Olivier

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**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\
**Post date:** [March 22, 2023, 12:32pm UTC](https://ask.bioexcel.eu/t/janssen-ligand-tutorial-why-no-h2hpolar-flag-in-atoms-to-morph-py/4210/2 "2023-03-22T12:32:58Z")

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I usually let polar hydrogens go via dummy transition, because these atoms might be involved in forming hydrogen bonds, i.e. I try to avoid hydrogen positioning in one molecule based on the coordinates of another. It should have minimal effect on the perturbation size, as there is another hydrogen occupying the same space in another molecule.