# Understanding the options of atom mapping and ligandHybrid

**URL:** <https://ask.bioexcel.eu/t/understanding-the-options-of-atom-mapping-and-ligandhybrid/4023>\
**Category:** pmx\
**Created:** [December 9, 2022, 4:35am UTC](https://ask.bioexcel.eu/t/understanding-the-options-of-atom-mapping-and-ligandhybrid/4023 "2022-12-09T04:35:43Z")\
**Posts on this page:** 1\
**Showing post:** 17

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**Author:** ![s.pallav](https://avatars.discourse-cdn.com/v4/letter/s/5f8ce5/32.png) [@s.pallav](https://ask.bioexcel.eu/u/s.pallav)\
**Post date:** [January 31, 2023, 6:42am UTC](https://ask.bioexcel.eu/t/understanding-the-options-of-atom-mapping-and-ligandhybrid/4023/17 "2023-01-31T06:42:05Z")

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> [@vgapsys](#):
>
> It is not published, you will need to try it out.

Hi Vytas,  
I tried it and it does helps. Now the question is to what extent one scales the dummy masses or the angles or the dihedrals? I used a pretty large number(100) for masses, angles and dihedrals and everything seems to be fine with it. But then it would be unrealistic for a dummy atom to have a mass of 100.008.

And for the simulations I had encountered LINCS error, I also used [https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/3?u=s.pallav](https://ask.bioexcel.eu/t/relative-constraint-deviation-after-lincs/2496/3) all-bonds in constraints and the simulation seems to be fine.  
Regards,  
Pallav

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