# Pmx ABFE ligand only simulation set-up

**URL:** <https://ask.bioexcel.eu/t/pmx-abfe-ligand-only-simulation-set-up/3800>\
**Category:** pmx\
**Created:** [July 11, 2022, 6:43pm UTC](https://ask.bioexcel.eu/t/pmx-abfe-ligand-only-simulation-set-up/3800 "2022-07-11T18:43:06Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![k-zator](https://avatars.discourse-cdn.com/v4/letter/k/5daacb/32.png) [@k-zator](https://ask.bioexcel.eu/u/k-zator)\
**Post date:** [July 11, 2022, 6:43pm UTC](https://ask.bioexcel.eu/t/pmx-abfe-ligand-only-simulation-set-up/3800/1 "2022-07-11T18:43:06Z")

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Hi,

I’m trying to set up ABFE calculations for a guest-host system in water following the pmx abfe functionality. The complex works, although has some trouble minimising. I let it generate the guest-host constraints for the FEP step automatically.  
I was then hoping to run the second arm of the calculation with guest molecule (Glycine anhydride) only but I was not sure how to impose the restraints then, and could not find any pmx documentation on the matter.  
Clearly using the original set does not work but then am I free to choose any heavy atoms?  
I tried running a calculation but it didn’t seem to restrain the position as found in .xtc and the simulation stops prematurely without a clear error (Segmentation fault (core dumped)).

Thanks in advance!  
Katarzyna Zator

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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:** [July 11, 2022, 6:50pm UTC](https://ask.bioexcel.eu/t/pmx-abfe-ligand-only-simulation-set-up/3800/2 "2022-07-11T18:50:01Z")

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It is not clear why you would want restraints in the guest-only leg of the thermodynamic cycle. One usually only needs to remove relative rotation+translation of the guest with respect to host for the host-guest branch of the cycle.

Vytas

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<div class="post-metadata">

**Author:** ![k-zator](https://avatars.discourse-cdn.com/v4/letter/k/5daacb/32.png) [@k-zator](https://ask.bioexcel.eu/u/k-zator)\
**Post date:** [July 11, 2022, 7:33pm UTC](https://ask.bioexcel.eu/t/pmx-abfe-ligand-only-simulation-set-up/3800/3 "2022-07-11T19:33:48Z")

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Ah, I was under the impression they were both done explicitly as diagrams are usually drawn so.  
How can I calculate the rot+trans contributions then?

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<div class="post-metadata">

**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\
**Post date:** [July 18, 2022, 7:53am UTC](https://ask.bioexcel.eu/t/pmx-abfe-ligand-only-simulation-set-up/3800/4 "2022-07-18T07:53:40Z")

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Analytical expression for the removal of rot+trans degrees of freedom is derived here: [https://pubs.acs.org/doi/full/10.1021/jp0217839](https://pubs.acs.org/doi/full/10.1021/jp0217839)

pmx calculates it when setting up the abfe and prints out to a separate file.