I got this (see picture) when save the result of clefts.

I used Windows 8.1, and PyMOL 2.4 win64 portable python 27 from pymol.org, NRGsuite 2.48l 64bit, I have installed all version of MVC++.

Need your help, please.

Thanks

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.

I’ve encountered an issue while installing NRGsuite. I got the suite from the NRGlab website; I’m posting here since their GitHub repository doesn’t have issues enabled, and I’m hoping that you’ll be able to help as a (former?) member of the group.

The details: I attempted the installation on my 2014-era MacBook Pro, running fully updated Big Sur (11.6.5). My pymol is a fresh install via Homebrew. If I attempt to install NRGsuite without python_tk installed, the installation succeeds, but the plugin fails to load, giving the error “No module named '_tkinter’”. After installing python_tk, pymol hangs on exiting, and crashes on attempted restart. Here’s a portion of stderr:

0   CoreFoundation         ...   __exceptionPreprocess + 242
1   libobjc.A.dylib        ...  objc_exception_throw + 48
2   CoreFoundation         ...  -[NSObject(NSObject) __retain_OA] + 0
3   CoreFoundation         ...   ___forwarding___ + 1448
4   CoreFoundation         ...  _CF_forwarding_prep_0 + 120
5   libtk8.6.dylib         ...  etRGBA + 50
6   libtk8.6.dylib         ...  SetCGColorComponents + 124
7   libtk8.6.dylib         ...  TkpGetColor + 543
8   libtk8.6.dylib         ...  Tk_GetColor + 143
... etc...

libc++abi: terminating with uncaught exception of type NSException
Abort trap: 6

I’m wondering if this might be some sort of module version compatibility thing. Anyway, I’m hoping to be able to find a solution. It’d be a shame if folks with somewhat older Macs couldn’t use the programs. I’d be happy to help in any way - more error output, trying solutions, whatever.

Thanks!

This happened on my Windows 10 for NRGSuite 2.48i (PyMOL 1.x) or NRGSuite 2.48l (PyMOL 2.x). Where is GetCleft's default location on Windows? How to solve this problem?

Thank you