The problem of druggability sites in drugui

[forever-up]

Issue Description:

I'm attempting to reproduce the druggability analysis from the paper "Precise druggability of the PTH type 1 receptor" using the specified probe mixture ratios:
Isopropanol (16%）Acetamide (14%)Acetate (14%)Isopropylamine (14%)Isobutane (14%)Imidazole (14%)Benzene (14%)

After completing the simulation, I executed python newscript_v7.py, but no druggable sites were identified. The output showed:
text
dg_IPRO was parsed in 1.10s
@> Searching probe binding hotspots with deltaG less than -1.00 kcal/mol (~5 folds enrichment).
Traceback (most recent call last):
File "probdx.py", line 237, in
calcDruggability(prefix, probe_grids, **parameters)
File "probdx.py", line 181, in calcDruggability
dia.perform_analysis()
File "druggability/dia.py", line 878, in perform_analysis
self.identify_hotspots()
File "/druggability/dia.py", line 447, in identify_hotspots
raise ProbeError('No hotspots found with binding free energy '
NameError: global name 'ProbeError' is not defined
Observations:
Visual inspection of the trajectory confirms probe density around the protein surface
the druggui VMD interface ，several hotspots is found,but The GUI version cannot process imidazole or benzene probes
Questions:

I have run “python newscript_v7.py” in other systems before, and successfully output dg_site_*.pdb. However, when running it in the pth system, it shows no sites, but the vmd gui can output output_site_3.pdb. What is the problem?

[Cventura18]

What are the probes you selected in python newscript_v7.py and the probes you selected for the druggability simulations?

[forever-up]

@Cventura18 Thank you very much for your reply，in the python newscript_v7.py ，the probes are "probes = ['IPRO', 'ACAM', 'ACTT', 'IPAM','IBTN','IMID','BENZ']",When I run this script, I find that the dx file is all 0 0 0. I have no choice but to use the vmd gui page of drugui to run it. However, the vmd gui page can only generate dx files for 5 types of probes, and cannot handle BENZ and IMID.

[Cventura18]

@forever-up it seems that only IPRO is being parsed, but the other probes are not. I believe the probes in newscript_v7.py don't match the probes in the pdb and psf file of PTH you have generated.

[AnthonyBogetti]

Hi @forever-up, was your issue resolved? If so, please close the issue. Thank you.