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CBDD / openduck

Open-source DUck (Dynamic Undocking)
http://www.ub.edu/bl/undocking/
Apache License 2.0
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Tests and yaml templates #12

Closed AlvaroSmorras closed 1 year ago

AlvaroSmorras commented 1 year ago

Some first test from people in the group managed to find small bugs, but i decided to create a small test for 'all' systems so we can have a quick pass for the versions. It is not really a CI, but will work for the moment (I hope). I have also added some templates for the yaml inputs.

AlvaroSmorras commented 1 year ago

I found the error. iWrap moves the box coordinates so the origin (left, bottom, front) to 0,0,0 but messes with the chunk imaging in the PBC. With the nmr restraint to keep the hydrogen bond in-place, the system explode as it needs to fulfill the 2.5 distance across the water-box instead of going through the PBC. I have added a centering step through cpptraj after the minimization and changed the references for the restraints so everything is ok now. This didn't happen with the MOE implementation, as it builds the input coordinates and topology through tleap and tleap centers the box with this conditions by default. I have not found an easy way to do it through PDBfixer before the generation of the inpcrd.