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Bacterial extracytoplasm and SiaP
https://www.rcsb.org/structure/3b50 Characterization of the N-acetyl-5-neuraminic acid-binding site of the extracytoplasmic solute receptor (SiaP) of nontypeable Haemophilus influenzae strain 2019...
View ArticleGMML to GMML2 phases
Creating GMML2 from GMML1 rationale and approach. GMML1 was essentially two designs living together. The new and old “Central Data Structure” design. What became GMML2 was created in the...
View Articlevdw parameter modifcation glycam aggregation
So there is a known issue with vdW interactions: van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD...
View ArticleCluster Slurm Jobs Submission scontrol hold release sinfo
Submitting to specific nodes: sbatch –exclude node[001-008] submit.GPU.thor.sh sbatch –nodelist node010 submit.GPU.thor.sh Holding jobs in the queue: This allows you to have jobs in the queue that...
View ArticleDev env series of issues
Issue 1: webdev@o-gw-grpc-delegator:/programs/gems/gmml$ git push The authenticity of host ‘github.com (140.82.121.3)’ can’t be established. ECDSA key fingerprint is...
View ArticleRunning out of space in the glycam residue nomenclature
I’m adding bacterial sugars to gmml and have hit the limit of the current glycam residue nomenclature: https://glycam.org/docs/forcefield/glycam-naming-2/index.html e.g.: No linkage code found for...
View ArticleRebasing in git
Tobias is trying to convert/rebase me to the git church of rebase: rebasing topic onto master A---B---C topic / D---E---A'---F master results in B'---C' topic / D---E---A'---F master which then allows...
View ArticleDatabase versioning from Tobias
Writing down a couple of thoughts on databases before I (Tobias) forget them; Soft deletes are really useful and prevent many a catastrophe. Just a column saying ‘deleted’ that’s checked instead of...
View ArticleRunning the Django pre-push tests can be run like this:
In the devEnv, from v2: bash bin/connect.sh django django That script brings you to the correct dir to run the tests.There is also a way to connect using docker exec + args. If you use that you need...
View ArticleChanging number of MD or minimization steps in dev env
Set number of steps in MDaaS: tl;dr hacky version that works for now, but will git track so be careful: In $GEMSHOME/External/MD_Utils/scripts/Run_Multi-Part_Simulation.bash Change:...
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