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**Is your feature request related to a problem? Please describe.**
The AM1-BCC charge scheme is fairly popular in drug discovery, but as far as I can tell, only Amber and OpenEye toolkits can gener…
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I see that there is some submission guidance for new building blocks and links at https://github.com/marrink-lab/polyply_1.0/wiki/Submit-polymer-parameters and https://github.com/marrink-lab/polyply_1…
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I'm working on adding an example to set up and run the entire FreeSolv set (in [this branch](https://github.com/choderalab/yank-examples/tree/freesolv/examples/hydration/freesolv)), and noticed that t…
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We need to trap bond order information for small molecules.
We can do this either through extending the MDTraj Topology object in Topography, or by switching to the OpenMM Topology in Topography.
…
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The Easy modron maze is a 4x4 rooms, the Medium is 6x6 and Hard 8x8. The maze difficulty is reset in the control/engineering room. You can rest in the antechamber, in Nordom's room, and in the Wizard'…
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### Comment:
This is an idea that's been mentioned a few times - with some effort, AmberTools could be released in bits vs. a single monolith that causes conflicts with other packages in users' envir…
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I'm attaching a serialised system of two phosphatidic acids parameterised using GAFF2 (ANTECHAMBER via phenix.elbow, for the record). I realise part of the problem is that they're non-physiological (a…
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When I run the absolute calculation protocol, I got the error below
```
/home/juyong/apps/amber18/bin:/home/juyong/anaconda3/envs/yank/bin:/usr/local/cuda-10.1/bin:/appl/anaconda3/envs/openmm_env/b…
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The mass assigned to dummy atoms needs fixing. The Lennard-Jones terms need to be checked.
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hey man,
It's likely that `parmed` (script) does not has function to quickly convert format.
`parmed -p rna.parm7 -po rna.mol2`.
If I don't miss anything here, should this be in todolist?
hainm updated
8 years ago