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Discngine / fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).
MIT License
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<mdpocket> analysing snapshot 46! No Pockets Found while refining #92

Closed H-EKE closed 9 months ago

H-EKE commented 1 year ago

Hi,

I am trying to look for pockets in a long MD trajectory (dcd format). When I use md pocket, I get always the following error for 70 % of the frames:

analysing snapshot 86! No Pockets Found while refining ! No pocket to reindex. ! No pocket to reindex. Also, once that analysis is done, the mdpout_freq_iso_0_5.pdb and mdpout_freq_iso_0_8.pdb are empty. Would you know where is the source of error?
louetadelie1 commented 1 year ago

I had a similar problem on a trajectory, which was odd because when I extracted a pdb file at each ts for the same trajectory and fed it to fpocket, I got good results. Has anyone found a solution to this issue?

H-EKE commented 1 year ago

Hi @louetadelie1 ,

I tried to mail the developers but I didn't receive any answer. If I figure something, I'll let you know

DAlvGar commented 1 year ago

Hi,

Could it be that the trajectory is not correctly aligned over a reference frame? It won’t detect the pocket otherwise.

Cheers, Daniel

H-EKE commented 1 year ago

Hi @DAlvGar ,

Thanks for your reply. My trajectory is well aligned. My problem i think is more related to the flexibility of my pocket. I have tried several approach to align the trajectory and nothing seems to work

pschmidtke commented 10 months ago

without a few frames that are in question , an input file and the command line (parameters) & version of fpocket you used I won't be able to comment much. There can be plenty of reasons for this to happen unfortunately.

H-EKE commented 10 months ago

Hi @pschmidtke

Thanks for your reply. Could it be possible to contact you by mail with all these details?

pschmidtke commented 9 months ago

sure, my first name + "." + my family name + my company name + ".com"