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Hi！
when I run "packmol-memgen --pdb 1bl8.pdb --lipids DOPE:DOPG --ratio 3:1 --keepligs", followed error thrown.
Traceback (most recent call last):
File "/root/anaconda3/bin/packmol-memgen", lin…
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I am having a lot of trouble finding clear direction on how to incorporate the packmol extension for Avogadro. This appears to be a common trap for new users - can someone pretty please provide idiot …
js598 updated
8 years ago
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I'm trying to replicate evaluator defaults (from the sage paper), through:
```python
topology = pack_box(
molecules=[solvent_offmol],
number_of_copies=[2000],
…
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@davidlmobley, can you take a look at [this failing test](https://travis-ci.org/choderalab/openmoltools/jobs/133226140#L2781-L2795) in `packmol` on `master`?
```
=====================================…
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Hi,
I am trying to repeat this tutorial: https://github.com/MobleyLab/drug-computing/blob/f38a4148e9e70238c88fc8110d95b34688f02838/uci-pharmsci/lectures/SMIRNOFF_simulations/mixture_simulations.ipynb…
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### Comment:
Hi everyone,
I never really got into the ambertools conda package. Checking it out, realized that the packmol package included in AmberTools is being patched out, and replaced with th…
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Trying to solvate a small molecule from trajectories or straight from PDB files for whatever reason inputs bond orders that are greater than 3... Any idea why this might be happening? Here's a short b…
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- [x] I read [the conda-forge documentation](https://conda-forge.org/docs/user/introduction.html#how-can-i-install-packages-from-conda-forge) and could not find the solution for my problem there.
…
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Using the packmol-memgen tool creates the membrane, but when loading the system into tleap you get a ton of FATAL errors when tleap cannot read the Atom type for the lipids, salts, and waters created …
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Attached are VMD views of my protein after completing step 4 of the tutorial and visualizing the pdb + prmtop file.
I used VMD to select the center lipids, identified their resids, and then used the …