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Hi, I have the following problem.
I want to create a simulation in which, in addition to the protein structure, there are several different small ligands. For this purpose, to assign them a force fie…
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Hello, I was wondering if it is possible to create a Forcefield using both caribou and sofa caribou.
I'm having a bit of a headache understanding where to start.
The idea would be to inherit from …
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#### Подробное описание проблемы
Если бить священника телескопической дубинкой или батоном охраны на хелпе. Голоурон будет проходить.
#### Что должно было произойти
Броня не пробита.
#### Что …
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**Describe the bug**
I'd like to be able to write amber parameter files using interchange from openff-toolkit. However, no bond information is included in the water xmls leading to failure.
**To …
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**Describe the behavior you would like added to mBuild**
MosDef currently provides an atom type xml section, and this section has an entry for name. The name is disregarded when writing the forcefie…
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Force field residue template generators must create ` _TemplateData` objects to handle molecules they parameterize. For GAFF or openforcefield small molecule force fields, this step can take a signifi…
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Seems like the forcefield description of water [**water.def**](https://github.com/numat/RASPA2/blob/master/molecules/TraPPE/water.def) in TraPPE forcefield folder is not entirely correct:
- The att…
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Hi,
I try to simulate a protein-protein docking between two proteions, one is a mulimer membrane protein which need to be restrained(chain A-I), another is a ligand protein which need move freely, …
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Hi,
This could totally be an issue of me learning the wizarding world of forces/forcefields...
When I parameterize a protein/ligand ahead of time with amber, I can get the implicit solvent work…