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Create a system with:
- a methionine-rich protein: [2MAT](https://www.rcsb.org/structure/2MAT)
- water (TIP3)
- ions (Na+, Cl-, K+, Mg2+, OH-)
- methanol, ethanol and urea (why not)
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**Describe the bug**
Carboxylate functional groups are read incorrectly from mol2 files produced by Amber/tleap. Carboxylate bond orders are specified as 1 such that the total charge of the functiona…
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@dominicrufa and I were trying to run repex on the endstates of a capped amino acid transformation (ALA->THR) (using the new [RepartitionedHybridTopologyFactory in perses](https://github.com/choderal…
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is there a docker to use it? the script installation fails for me
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Hello,
Is the parameter `use_short_tol` expected to not work on Windows? This issue is popping up in a unit test on a [PR](https://github.com/mosdef-hub/mbuild/pull/787) of another repo where we ar…
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Please find the attached tarball containing an input deck and two output log files, one for Mac which runs and one for Linux which fails with a segfault. Is there something wrong with my input file tf…
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I have a PDB with a protein solvated in hexane (with ions) and here you can see it before minimization. I make this system using **Packmol**:
Then I run the following code to do an initial minim…
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This is in the https://github.com/mosdef-hub/mbuild/blob/0.13.1/mbuild/packing.py file.
Packing fails in much larger systems unless the packing is not that dense, add the below variables would give…
bc118 updated
5 months ago
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**A summary of the question or discussion topic.**
Some simulation engines, such as CP2K and Cassandra, require a high precision of atomic coordinates when implementing fixed bonds and angles (@ram…
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**Describe the bug**
`Molecule.from_polymer_pdb()` gives an undefined stereochemistry error for the attached PDB.
[protein.zip](https://github.com/openforcefield/openff-toolkit/files/9815418/prote…