Question about ABFE using restraint search #329
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Hello there. The ABFE implementation is currently part of the Exscientia sandpit, so you'll need to use |
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Thank you so much for your quick reply! It is my fault I did not read it clearly. I am sorry. |
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Not at present. This is something that we plan to work on in the near future. |
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@lohedges |
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Hi @lohedges, This is the error message it showed: And here is my code: gro="output_setup/ejm31/com/05_npt_relax/05_npt_relax_out.gro" lig = BSS.Align.decouple(system[0]) protocol = BSS.Protocol.Production(runtime=0.01*BSS.Units.Time.nanosecond) restraint_search = BSS.FreeEnergy.RestraintSearch(system, protocol=protocol, engine='gromacs', work_dir='restraint_search') restraint_search.start() restraint_search.wait() I just want to report this issue. |
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That's strange. I didn't write this part of the code so will ask @fjclark to comment when he's back. Ideally this should be interoperable and not dependent on specific naming of the topology file, which looks to be the problem here. I've checked the latest version of the code and the selection string appears to be identical. (Although there aren't the commented print statements, but maybe these are yours from debugging.) |
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05_npt_relax.zip |
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Many thanks, this will be really helpful. |
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Hi @jnutyj, thanks for reporting and for providing the files. I've tried to reproduce this locally using your script and the files provided, but it works fine for me. It looks like your issue is that MDAnalysis is failing to read the trajectory and topology, which causes the MDAnalysis universe object ( It would be good if the error message was more helpful - do you think the BSS warning about MDAnalysis failing to read the trajectory should be an exception instead @lohedges? Thanks! |
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Hi @fjclark, And here is my gromacs version: |
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Thanks! Turns out the issue is caused by using the latest version of GROMACS. When I upgrade to 24.2, I can reproduce this error. Printing the error inside the try/except block which raises the BSS warning shows: Because MDAnalysis 2.7.0 is does not support the newest GROMACS tpx format (see the relevant PR here). To get round this you need to install the latest development version of MDAnalysis, which is not available on conda forge. To do this, first remove your current version of MDAnalysis with This removes only MDAnalysis, but I think the behaviour is different if you use mamba (you can install conda in your mamba environment if so). Then clone the MDAnalysis github repo and install from source: Then your script should work fine with GROMACS 24.2. |
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Thank you @fjclark !!! |
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No problem! |
Hi,
I went through the tutorial in notebook for website, and everything is good. But when I download BioSimSpace, and ran in my local pc.
For the ABFE tutorial (04_fep/03_ABFE), it does not have "RestraintSearch" attribute in BioSimSpace.FreeEnergy.
It seems that this feature is not available anymore. If I want to search Restraints for Absolute binding free energy, how can I do that?
Thank you !
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