getting error while generating restrains for ABFE

[jjmallen]

Good day,

I am trying to generate restraints for ABFE and I am getting an error. May you please assist with this error, please find the attached document below.
test_run.txt

[jjmallen]

[lohedges]

@fjclark: Any ideas about this one?

[jmichel80]

@jjmallen - is this error message triggered with the inputs provided with the tutorial? Using the environment available at try.openbiosim.org ?

[fjclark]

Hi @jjmallen, thanks for providing the notebook. The first thing which jumps out is that it looks like you're trying to decouple an entire protein, which I assume is not intended? e.g. you have

system1[0].getResidues()

which shows a protein with 162 residues, and in the next cell you have

lig = BSS.Align.decouple(system1[0])
system1.updateMolecule(0, lig)

where lig is your entire protein. Try rerunning with the correct index for your ligand in these two lines.

The error seems to be due to the variance of a dihedral being 0, which might happen if both the "protein" and "ligand" anchors are in the same molecule.

If that doesn't fix it, please provide the input files and let us know exactly what you're aiming to do.

Hope that helps!

[fjclark]

Also, I should make the code robust by:

• Ensuring that anchors can never be in the same molecule
• Warning the user if they select the protein/water as the "ligand"
• Warning the user if they supply very few frames for fitting

I will wait until this issue is resolved before making these changes.

[fjclark]

Hi @jjmallen, did you get a chance to check that you were decoupling the correct molecule? We've added some checks in the latest version of BioSimSpace which should raise a warning if the decoupled molecule isn't sensible/ if you try to select restraint anchor points in the same molecule. Thanks.