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**Describe the bug**
Get an Index Error when running AssignLeaflets with a system built with AMBER forcefield. The membrane contains POPC.
**To Reproduce**
A minimal working example of code to …
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The distance calculations don't seem to be able to handle periodic boundaries, they probably should. Even with a centered and sane configuration, `linalg.norm` isn't going to give the minimum distanc…
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Hi,
MountainSort works fine on the synthetic data, but I get this error when trying to sort my own data.
This seems like a simple error.
Thanks.
`mlp-run mountainsort3.mlp sort --raw=raw.mda …
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```
Recently I have builded ossim and opencv, but i think ossimlanet will be widely
used in the icode-mda, so i want to know how to build ossimplanet
```
Original issue reported on code.google.com b…
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## Expected behavior ##
If an `Universe` is created with more than one trajectory file and a `MDAnalysis.transformations.fit.fit_rot_trans` transformation is added to it, it is expected that all fram…
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### Description of bug
I used the assembly command: spades.py --pe1-1 B5.R1.trim.fq.gz --pe1-2 B5.R2.trim.fq.gz -t 96 -k 61, 71, 77, 81 -m 760 --careful --phred-offset 33 -o ../spades/B5 . This comm…
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Currently this is needed to avoid issues with the MDA. This is slightly annoying. This could be avoided if we instead treated a lambda expression as a unary operator.
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I use go-msgauth/dkim to verify signatures in my internal MDA.
In my development environment, I had an issue where mail was backed up for a few days. Once I fixed the issue and resumed queue proces…
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## Problem ##
There is no example in the documentation that shows how a pair of LAMMPS data (topology) and dump (trajectory) can be loaded with the *format="LAMMPSDUMP"* option of the `mda.Universe(…
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Cannot read library(mda) in Mars.R because that library is only compatible with R 3.5+, and Sagemaker R scripts run on R 3.2.3.