Failed to finish the HSA job #8
Description
Hi, I got some issue when running SSTMAP 1.1.4 to do HSA, I put the running information as follwed. Can anyone help? Thank you for your time in advance.
Version: SSTMAP 1.1.4
Command: $ run_hsa -i nvt_heavy_production.gro -t nvt_heavy_production.xtc -l ligand.pdb -p topol.top -s 80000 -f 1000 -o testcase
The simulation is 100 ns, and the frames were save every ps and I took the 1000 frames starting from 80ns to run the HSA
Runing information:
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 3.42 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 0.70 seconds
Done.
Total time running init: 12.58 seconds
Reading trajectory for clustering.
Performing an initial clustering over 100 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 1000 frames.
Final number of clusters: 13
Total time running generate_clusters: 7.73 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 7.73 seconds
System information:
Parameter file: /SSTMAP/gromacs run/production tpr/SSTMap cal/NVT_heavy/nvt_heavy_production.gro
Trajectory:/SSTMAP/gromacs run/production tpr/SSTMap cal/NVT_heavy/nvt_heavy_production.xtc
Total Atoms: 75555, Waters: 23698, Solute Atoms: 4461
Number of clusters: 13
Writing PDB file containing all HSA region water molecules for entropy calculations.
Done.
Writing PDB files for all water molecules in each hydration site.
Done.
Total time running generate_data_for_entropycalcs: 0.16 seconds
Generating expanded cluster water files...
Running entropy calculation from extension module.
terminate called after throwing an instance of 'std::bad_array_new_length'
what(): std::bad_array_new_length
Aborted (core dumped)