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Hi all,
I have been running Tram on a set of biased and unbiased simulation data, and I argue the results are not converging but I cannot figure out why.
I have a set of 24 umbrella sampling simulati…
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@JonnyCBB
Hi Jonny,
I think I've found a bug - the unit cell atom list is generated from the pdb file after being put through PDBCUR (so that alternative conformations etc. are removed), but the asy…
kls93 updated
8 years ago
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I have another problem in understanding the output of dihistidine. I got 9 microstates for dihistidine in MCCE(four neutral, four with +1 charge and one with +2 charge). I am not sure why is it 19 in…
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some xxx linked glyciosylation terms appear to be
preceeded by
protein amino acid xxx-linked glycosy/galacto/mannosyl
etc. ylation, and some don't.
Reported by: ValWood
Original Ticket: "geneontol…
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Would it be possible to add a variant of the contact feature which is a continuous switching function, such as a tanh, instead of a step-function?
For clarity I'm thinking of something like:
0.5*(ta…
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So, I just tried a very large proposal of transforming erlotinib into gefitinib. A couple things:
1. While it didn't die in dynamics (1000 steps of verlet at 300K, no NCMC), the potential did get much…
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Following discussion (Issue #232) a selection of target compounds for the second round of biological evaluation for the triazolopyrazines.
This compound is a representative example from the chiral et…
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Given `CC(=O)[C@@]1(O)CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C`, the babel-generated 3d molecules differ at two stereocenters from the Schrodinger Ligprep-generated molecule.
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The basic overview will be covered in the talk #5 . We will use interactive Jupyter notebooks to develop the problems. We will use clean notebooks as guides; participants can use the clean notebooks a…
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First from Sonya, then from me.
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General comments:
1a. I like Kyle's comment that for a method's paper there is maybe too much analysis of the kinase data, especially considering that the anal…