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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 on aligned AMBER trajectory in pdb format #93

Closed ghost closed 10 months ago

ghost commented 1 year ago

Hi, I am running mdpocket using this command line:

mdpocket --trajectory_file /storage/debarati/all_water_closed.pdb --trajectory_format pdb -f reference_water.pdb The trajectory has 6500 frames all in that single pdb

How to troubleshoot please help? Thanks

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pschmidtke commented 10 months ago

The supported trajectory formats for the trajectory_format flag are: Supported trajectory formats Trajectory format : Amber MDCRD without box information (crd)
Amber MDCRD with box information (crdbox)
NetCDF (netcdf)
DCD (dcd)
DESRES DTR (dtr)
Gromacs TRR (trr)
Gromacs XTC (xtc)

as stated when you trigger the help in the CLI or in the documentation. If you want to use a list of pdb files, you have to write them out separately and use a text file listing these by order (timeframe) with the mdpocket --pdb_list file.txt Hope that helps