![]() The ATM app is based on Python, similar to the PythonRL application, where we ship it with a specific python environment. Additionally, since these methods are usually applied to hundreds of molecules, it benefits a lot from the parallelization capabilities of GPUGRID, so if everything goes as expected, this could potentially send lots of work units. We are actively working now on testing and validating the ATM method so that we can start applying it to real drug discovery projects as soon as possible. Having the capacity to perform computational binding affinity predictions, particularly during drug lead optimization, is extremely beneficial. Measuring experimental binding affinities between candidate molecules and the targeted protein is one of the first steps in drug discovery projects, but synthesizing molecules and performing experiments is expensive. The benefits of ATM, when compared with other common free energy prediction methods (like the popular FEP), come from its simplicity, as it can be used with any forcefield and does not require a lot of expertise to make it work properly. This methodology falls under the category of alchemical free energy calculation methods, where unphysical intermediate states are used to estimate the free energy of physical processes (such as protein-ligand binding). The ATM method allows us to estimate binding affinities for molecules against a specific protein, measuring the strength at which they bind. designed for absolute and relative binding affinity predictions. The new ATM application stands for Alchemical Transfer Method, a methodology Emilio Gallicchio et al. Let me briefly explain what this new app is about. We are working on its validation and deployment, so expect more jobs to come on this app soon. Scheduler request completed: got 8 new tasks.īut it does seem to be working now, although it would have been nice to know just what was going on before.You‘ve already noticed that a new app called “ATM” has been deployed with some test runs. Off went the work request, and back came the reply: No tasks left by this time, but at least I'd see if there was anything different in the event log. It was early in the morning before I woke up again, and eventually I decided to get up and run it again to see what happened. So I turned off getting new tasks and the Net access, set up the BOINC options the way that I wanted, went to the web site and changed the venue and then went to bed, because of the 1 hour backoff. Next was to run it and see what happened.Īttached the "new" computer to the project, and it immediately used the default venue. Then I loaded up BOINC again, the easy part. I found one that was only a couple of versions earlier, so I spent the next few hours rebuild the OS and upgrading it to current. It's changed a lot since I looked last.Īnd I did put that into the sample config file that was in among the BOINC stuff, and read it.Īll that happened was that the event log then mentioned it, but there were no extra messages, which was disappointing.Īt this point I gave up for a few hours, but then decided to look at my collection of OS disks. Yes, I thought of the config stuff, and had a look. No override file, and the venue being used is "school" Update them on the main project web site and then issue an update on the main project from the manager and you should see that the site referenced in Boinc manager has changed to the main site. In your case that sounds like the test site. Boinc uses the preferences of the last project (time stamp) web site that you changed them on. ![]() ![]() Whatever is wrong is bound to be simple, and once I know, obvious.Īh, expected. Ubuntu is dishing up 7.6.31 if that's relevant. I've just uninstalled BOINC (Linux) and installed it again, with no change. The local prefs are correct, and I can't see anything else that would stop downloads. (May also be a problem with the other computer, and I just don't know it yet.) My original and main problem, is that I can't get one of the computers to download any tasks from the main site. I'm not sure if this has something to do with it. In both of my computers, this points to the test site preferences, and I can't get it to change to the main site preferences.īoth sites have recently been upgraded to the latest, (I'm told), server version. In the BOINC Manager, in Options > Computing preferences, there's a blue url at the top left for using web preferences.
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