Empty subdirectories after running run_snapshot.sh

[accibio]

Hi! I am trying to follow the Pharmmaker tutorial to generate pharmacophore models for a protein simulated with probes and analyzed using DruGUI. I have successfully run these three modules of Pharmmaker:

3.1. High affinity residues
3.2. Hot spots near high affinity residues
3.3. Focusing on hot spots at regions of interest

As mentioned in the tutorial, I have modified the highaffresid.dat and highAffHotspots.pdb files to include only the residues and hotspots lying in the region of my interest. However when I run the run_snapshot.sh script to generate snapshots, it creates a snapshot directory and multiple subdirectories (e.g. z.A.23.IPRO, z.A.24.IPRO etc.) based on the residues and probes lying in the region of interest. But the subdirectories are empty. How do I generate the snapshot files like outfr-1.dat, outfr-count, out-detail-res-1.dat etc.

Please help me identify the issue and resolve it. Thanks!

[jiyounglee22]

First thing to do is that upload dcd using VMD or pymol and check if any probe molecule stays in the hotspot you selected.

[accibio]

I had a look at the simulation. The IPRO probes remain in the region of interest throughout nearly the entire duration of the simulation.