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wolberlab
PyRod - Tracing water molecules in molecular dynamics simulations
Hello developers: I am trying to use pyrod with trajectory_analysis.cfg file. The trajectory_analysis.cfg file fellows: [directory] directory: [trajectory analysis parameters] center: 48, 40, 35 edge lengths: 35, 35, 35 topology:...
Hi David, I hope this message finds you well. Firstly, I would like to express my gratitude for developing the Pyrod on GitHub. I recently downloaded and attempted to reproduce...
errot
FileNotFoundError: [Errno 2] No such file or directory: '/hdd1/software/pyrod/pyrod/centroid/frames_0.csv' Traceback (most recent call last): File "pyrod.py", line 240, in ensemble_to_centroid(topology, trajectories, output_name, directory, debugging) File "/hdd1/software/pyrod/pyrod_lib/trajectory.py", line 578, in ensemble_to_centroid...
Dear David, I have obtained the 180 features by pyrod. Would ask you how to determine the features obtained by pyrod could be used for virtual screening. I also attacheed...
Hi.. I now installed the tool and want to see how use it. I did MD simulation for a protein using gromacs.. Should I use both pdb file and xtc...
Dear David, I hope this message finds you well. I am encountering problems while generating the combinatorial pharmacophore library. I have successfully acquired the super_pharmacophore.pml file using the trajectory_pharmacophore_combo.cfg and...
