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Acceptance Ratio: 0.0 #174
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I've tried setting |
I hadn't gotten a moment to answer this, but you just closed it... did you resolve this issue somehow? |
Hi @davidlmobley , thanks for your attention! After reading your paper more carefully, I realized that the default In this case, to validate the possible binding pose due to rotation of the toluene group, maybe a custom I'd like to try the implementation here: #164. |
Right, yes, we've found that for larger ligands (and those with rotatable bonds) the odds of finding a new reasonable pose just by rotating the whole ligand get really really low. So we often run into the issue you described. If you're just interested in where the aromatic ring points, then you want a torsional move; I very much agree. Will try to look at your PR soon, though I probably can't do much of a code review -- the students working on BLUES have graduated and I don't have someone currently developing it; I'd like to do so again, but that requires finding the right person first. Can I ask where you're based/in what group? Feel free to e-mail if you'd prefer. |
Hi, I'm testing BLUES with the
1H1R
ligand, which was shown to have two possible binding modes:I'm using the default protocol provided in the example. The BLUES simulation has run for 100 iteration, but the acceptance ratio is 0.0. Is there something I can do? Thanks!
Here are the input and output files:
temp.zip
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