Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Unable to run povme on my pdb #54

Open
Jahan-I opened this issue Feb 3, 2025 · 0 comments
Open

Unable to run povme on my pdb #54

Jahan-I opened this issue Feb 3, 2025 · 0 comments

Comments

@Jahan-I
Copy link

Jahan-I commented Feb 3, 2025

Hi, I am trying to run povme on my system but I am getting an error:
OUTPUTBASENAME: example_

PARAMETERS DEFINED


ABOUT TO LOAD RECEPTORS

Reading frames from 1X7R.pdb
Further processing frame 1
Further processing frame 2
Further processing frame 3
Further processing frame 4
Further processing frame 5

RECEPTORS LOADED

Generating the pocket-encompassing point field

Saving the point field as a PDB and NPY file
Point field saved to ./POVME_test_run/example_frameInfo/example_inclusion.pdb to permit visualization
Point field saved to ./POVME_test_run/example_frameInfo/example_inclusion.npy to optionally load for the volume calculation

Saving the contiguous-pocket seed points as a PDB and NPY file
Contiguous-pocket seed points saved to ./POVME_test_run/example_frameInfo/example_seed.pdb to permit visualization
Point field saved to ./POVME_test_run/example_frameInfo/example_seed.npy to optionally load for the volume calculation

Calculating the pocket volume of each frame

STARTING CALC VOLUME

Traceback (most recent call last):
File "/home/cmbc/miniconda2/bin/POVME3.py", line 2205, in
if name == "main": dorun = runit(sys.argv)
File "/home/cmbc/miniconda2/bin/POVME3.py", line 1970, in init
tmp = Multithreading([(index, pdb_object, parameters) for index, pdb_object in index_and_pdbs], parameters[NumProcessors], MultithreadingCalcVolumeTask)
File "/home/cmbc/miniconda2/bin/POVME3.py", line 146, in init
for item in inputs: single_thread.value_func(item, None)
File "/home/cmbc/miniconda2/bin/POVME3.py", line 1089, in value_func
coloredMaps = my_peel.color_povme_map(pts, parameters[GridSpacing], skin=color_skin_distance)
File "/home/cmbc/miniconda2/lib/python2.7/site-packages/POVME/packages/binana/peel.py", line 3397, in color_povme_map
minX = np.min(povmeMatrix[:,0])
File "/home/cmbc/miniconda2/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2618, in amin
initial=initial)
File "/home/cmbc/miniconda2/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)

But when I run povme on the basic example provided , it ran smoothly.
Kindly help me in resolving this issue as I am facing this problem since 2 days.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant