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Morning everyone,
I'm working with h5 trajectories of a system that involves 2 proteins with 3 Zincs in different coordination states. These are prepared with Tleap and simulated using OpenMM. In t…
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When processing the attached molfile of a metal carbene complex, OpenBabel reports the sum formula incorrectly as C13H14BrF6N5PPt instead of correct C13H13BrF6N5PPt (using the stand-alone OpenBabel …
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Here's another example of a hard geometry optimization problem.
Psi4 1.3.2 crashes/segfaults; @psi-rking's pyoptking also gives up.
```
import optking
memory 8 gb
molecule {
Mn -1.1985…
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OPTIMADE specification v1.0.1 defines a structure as a set of sites, occupied by mixtures of atoms, with each atom described by its chemical type, mass and occupancy (proportion in the mixture). Means…
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Evaluate and track porting of PhET sims that I've worked on, from Java to HTML5.
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Here are several PDBs of the human adenosine receptor ADORA2 bound to various ligands, made using X-ray crystallography:
https://tinyurl.com/yc7bckxx (links to rcsb.org).
Have to come up with a …
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I heard that there is some sf than can be used in metal ions(Mg,Se,Zn...) docking in AutoDock Vina, But I couldn't find it in manual.
Is there anything to do with ` v = Vina(sf_name='vina')`?
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Over the next couple of days (unless something unforeseen happens) I have time to make a start with building the add-on from scratch. Getting it to match the working features of BB2 will take a while…
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OpenMM's topology objects and readers/writers don't provide enough chemical information to actually parameterize small molecules nonstandard biopolymers, post-translational modifications, glycosylatio…
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Reserved the handle @_atomone (following Gnoland's handle nomenclature, @_gnoland) and have created a first direction for ATOM ONE's brand identity.
The handle is transferrable at the team's reque…