Input coordinates for step d should be taken from d_sopt - input (ported from gitlab)

rinikerlab / reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.

https://rinikerlab.github.io/reeds/

MIT License

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Input coordinates for step d should be taken from d_sopt - input (ported from gitlab) #5

Closed SalomeRonja closed 3 years ago

SalomeRonja commented 3 years ago

by @candidechamp :

Adjust the paths to the correct input.

[x] also for step a

SalomeRonja commented 3 years ago

comment from @SchroederB: I'm considering how to solve this. In principle it's not a bug. The input coordinates are used from d_sopt/sopt1/input and not as it was expected from d_sopt/input. But in the module script d_sopt/sopt1/input is generated from d_sopt/input. I wonder if we should remove the redundancy or simply life with it :)

SalomeRonja commented 3 years ago

comment from @SchroederB: what is your oppinion @candidechamp ?

candidechamp commented 3 years ago

@SalomeRonja I actually fixed this "bug" in my latest pull request. It now points to the cnfs in the directory from which we expect them. (At least if what i did works well).

As you can see, we had already talked about it with Benjamin a long long time ago (when the original gitlab commit was made, and I think our idea back then was that it shoud be changed).

SalomeRonja commented 3 years ago

@candidechamp great, thanks for the quick feedback. I'm currently testing your latest pull request, so I'll close this issue once I do the merge.

candidechamp commented 3 years ago

@SalomeRonja Ok thanks a lot for this.