Segmentation fault (core dumped)

[caiyingchun]

I got this

run_hsa -i center.pdb -t center_converted.nc -l ligand.pdb -p center-out_cms_nb_parms.txt -s 0 -f 100 -o center
Initializing ...
Obtaining non-bonded parameters for the system ...
Total time running generate_nonbonded_params: 0.48 seconds
Done.
Assigning hydrogen bond types ...
Total time running assign_hb_types: 3.24 seconds
Done.
Total time running __init__: 6.13 seconds
Reading trajectory for clustering.
Performing an initial clustering over 10 frames.
Reading trajectory to obtain water molecules for each cluster.
Refining initial cluster positions by considering 100 frames.
Final number of clusters: 0
Total time running generate_clusters: 10.72 seconds
Total time running initialize_site_data: 0.00 seconds
Total time running initialize_hydration_sites: 10.72 seconds
System information:
        Parameter file: /data/sdd/home/workspace/SSTMAP/desmond_md_job/center.pdb

        Trajectory: /data/sdd/home/workspace/SSTMAP/desmond_md_job/center_converted.nc

        Total Atoms: 71228, Waters: 21077, Solute Atoms: 7997

        Number of clusters: 0

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: 0.03 seconds
Generating expanded cluster water files...
Segmentation fault (core dumped)

I noted that the number of clusters was 0. And I tried many times with different number of frame, but got the same results.

[Yeonji-Ji]

Hello, Sorry that it took so long to answer, but I don't understand why it happened. Could you send me the files so that I can figure it out?

[wutobias]

Not sure if it is related, but in the past these kind of issues were due to wrong numpy version. Make sure your conda environment has numpy v. 1.14. See here for context.

[caiyingchun]

@Yeonji-Ji I tried many times and found its related to the reference structure for run_hsa and parameter -g for run_gist. Sometimes it successed for both run_hsa and run_gist, while sometimes it failed for either run_hsa and run_gist. So I wonder how to generate the right reference ligand structure to run? Do it need to align the trajetory before running? Thanks.

[caiyingchun]

@wutobias Its not related to numpy version.

[hshams522]

I have a similar issue but get 'Aborted (core dumped)'. If I don't have a ligand in my structure but need solvation analysis of the binding site, can I give binding pocket residues as my ligand? Thanks!

[hshams522]

Hi Yeonji,

Unfortunately my files are confidential but I can try to reproduce the error using some public data and send it back. Aside from that, a general question I have with SSTMap is whether it can analyze solvent in the absence of ligand, e.g. like 3D RISM. And if so, should the ligand be the binding pocket residues around which we'd like to predict conserved water positions?

Of note, we have tried switching our platform to Ubuntu and updated gcc and conda and nothing really helped.

Thanks, Hengi

On Wed, Oct 26, 2022 at 10:45 AM Yeonji-Ji @.***> wrote:

@caiyingchun https://github.com/caiyingchun Sorry for the late response. Could you send the files to @.*** so I can try with my computer?

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