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We're suddenly getting a peculiar error relating to an unknown module `tables` in a delayed import in openmoltools which seems related to mdtraj: https://travis-ci.org/choderalab/openmoltools/jobs/659…
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I think one thing that's been a big headache for people who are trying to make reproducible clones of simulations has been getting a fixed number of solvent molecules. I think It would be nice to add …
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The build for `packmol` fails because `build.sh` tries to use `/usr/bin/gfortran`; note that this is often installed in a different location on `osx` (e.g. `/usr/local/bin/gfortran`):
```
BUILD START…
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I was actually hoping to have an example that packaged the entire FreeSolv small molecule database into a single OpenMM ForceField-compatible ffxml file, since we could use this for various OpenMM-dep…
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The build dies partway through trying to build `msmbuilder`:
```
conda build --output msmbuilder
Traceback (most recent call last):
File "build-all.py", line 24, in
build('msmbuilder')
File …
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Why is the repo like 100MB to download?
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- [x] @jchodera: both assaytools and assaytools-dev are named "development snapshot" in their description
- [x] @danielparton one of either `clusterutils` or `cluster-utils` is old and should be remov…
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I think we might run into an issue if we run gaff2xml twice on, say, a host and guest molecule separately. The resulting `ffxml` files can potentially have the same atom names, and OpenMM's `ForceFie…
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Many of the mdtraj 1.2.0 binaries have gone missing from the main channel. See in particular the linux and OS-X builds, which now only have py26 versions.
https://binstar.org/omnia/mdtraj/files?versio…
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Currently mdtraj automatically names the chains in PDB files in alphabetic order, starting from 'A'. I ran into a situation recently where I needed to use a different naming convention due to some oth…