lmorency/NRGsuite

It is not working using PyMOL built by python 3.7

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o7o commented

Hi, I hope this project can be continued and evolved because it is useful, very, for me to teach and deliver simple computational skill to my students. It is based on project, so make it simple to return and recompute using others ligands.

First thing, I faced trouble using NRGsuite GUI (2.48l) with PyMOL version 2.4.x above (from Schrodinger) that I think it is built from python 3.7 as it said in its repo. I have tested it on my MacOS (10.14 and 10.10) or Linux (Ubuntu 14.04) or Windows (7 and 10), but it did not work as usual. I used PyMOL 1.7.x in Windows and PyMOL 2.x built from python 2.7 in MacOS and Linux in order to make NRGsuite work smoothly. I need this NRGsuite GUI version for teaching in class.

The second one, if it is possible, I woluld like to request some features in NRGsuite developer to evolve it to the next level, like P*RX (I think, one of the successful example) but I can not get the project and save grid feature in it.

These are my requests:

  1. Multiple proteins and/or ligands running (normal and/or reverse simulation). I think it need just a few step more because https://github.com/padideee/Wrapper_FlexAID has been made
  2. Optional choice to save the process log of Simulation.
  3. Semi-automatic to choose center of partition cleft to ligand position, I found the differencce result from sphere and cleft, it is very good point for create computational grid for getting faster and precise the prediction result of ligan-protein complex interaction.
  4. The optional button to choice automatic name maker for folder of Simulation result beside its default naming, such as "default date"-"custom name addition"
  5. Button to choice run single simulation or replicated simulation (then only shows the best one in the end process) better than multiple click on Run for the same condition of simulation (including the same protein and ligand used).

Thanks for your effort and this software, I like it.