search

Electrostatics / apbs

Software for biomolecular electrostatics and solvation calculations
http://www.poissonboltzmann.org/
Other
91 stars 24 forks source link

Similarity Tool #140

Open sbembenek18 opened 3 years ago

sbembenek18 commented 3 years ago

While I am able to successfully use the similarity tool over a range of small molecules, when going beyond a grid size of 65 (for the input DX files), for example 97, 161, I consistently get a segmentation fault.

sbembenek18 commented 3 years ago

I wanted to follow up on this and see if this issue has been resolved. thanks.

sobolevnrm commented 3 years ago

Sorry; I have not done anything about this yet.

sbembenek18 commented 3 years ago

No worries. Thanks.

sbembenek18 commented 2 years ago

Following up on this. It doesn't seem to be simply a grid size issue as I just got the segmentation fault error for grid size of 65 and had to drop it to 33 to get the similarity calculation to run correctly. Look forward to your thoughts. Let me know if sending the DX file would be useful (can't attach here).

sobolevnrm commented 2 years ago

Yes, providing the DX file and a description of how you're invoking the code would be very helpful. You should be able to ZIP the DX file and attach it here. Thanks.

sbembenek18 commented 2 years ago

I am running the command as (per the attached file) -->

similarity --format dx --scalar1 ref_mol_pymol-generated_65.dx --scalar2 ref_mol_pymol-generated_65.dx

(Just a quick check against itself.) When the grid is 65 it gives a segmentation fault (see attached output.txt), but runs fine when the grid is remade to be 33. I had a similar experience with other molecules where lowering the grid size fixed the issue. In general, I have not been able to go past a grid size of 65.

The DX file is made through Pymol using the APBS plugin (I have attached the resulting APBS input file).

The DX is of a small molecule and so the PQR file is not made with PDB2PQR. Nonetheless, the resulting isosurfaces and related made from it (via Pymol) are as expected -- no issues there.

Thanks. for looking into it. Let me know if I can provide more info.

output.txt pymol-generated.in.tar.gz ref_mol_pymol-generated_65.dx.tar.gz

sbembenek18 commented 2 years ago

Quick follow up in this: we're you able to re-produce the error?

sobolevnrm commented 2 years ago

I have not had time to try; sorry. I am also not sure when I will have time to try. I am keeping this issue open in the hope that I will get time in the future but the similarity tool has never been a key feature of the code and, as such, this has lower priority than other issues.

sbembenek18 commented 2 years ago

OK. Thanks. Is there another way that you're quantitatively comparing the DX grids from APBS if not with the similarity tool?