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Not to be confused with the other portal 1 beta style suggestions, which mainly took from the age of development where many things weren't completely textured, and bluish bits were turquoise and that …
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On Linux, using the b7 snapshot, when I run
"perl Makefile.PL" or "perl Makefile.PL PREFIX=$tree" I get:
Can't build and link to 'openbabel'
If however, I edit the file to take into account the…
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Modify Foyer to accept a specific itp file and specific rules.py file (also make it so you can easily define rules in a notebook and pass them to foyer).
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I've noticed that many example don't specify in the options `softcore_beta: 0.0`, should we add it in all of them? Does it make sense to change the default value of that parameter in `AbsoluteAlchemic…
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```
darkunderdog [12:56 PM]
Is there a plugin for SSC lets people import their Character data from their file into the server?
darkunderdog [1:00 PM]
I like SSC for plugins that use SSC like Jumppad…
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I tried running 25 ns md with the script from the attached zip ([opennm_nan.zip](https://github.com/pandegroup/openmm/files/583926/opennm_nan.zip)) on several frames from a gromacs md run (which have …
sroet updated
7 years ago
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With AmberMini v16, there are a number of FF files which got moved into a folder called "oldff/leaprc.{file}". A number of our examples make use of some of these files and expect them in the standard …
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At the moment I cannot test locally out of the box.
I did a
```
pip install --upgrade .
```
but because this does not install [PyBOL](https://github.com/ianmkenney/PyBOL) (manifest) running the te…
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Refer to the literature, and this: http://ambermd.org/antechamber/gaff.html#test1
May be helpful in our structures when don't need to be that accurate at the atomic level. Current sulfur structures …