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Currently, in the water bridge analysis module, the user needs to give the name for the hydrogen bond donor heavy atom and the hydrogens were found via a simple distance search. I'm interested in usin…
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Either I fail to understand how ParmEd intends to handle the `nonbond_params` section in a GROMACS topology file or I've come across a bug. I'm working with a system in which I'm trying to assign i-j …
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**Describe the behavior you would like added to Foyer**
After discussions with @umesh-timalsina and @daico007 , It occurred to me that we might be able to include various grammars as plug-ins for foy…
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**Describe the behavior you would like added to Foyer**
Right now, in `test_opls.py`, the script crawls through a directory and tries to find either a combination of TOP & GRO files or a MOL2 file fo…
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- [ ] I believe this to be a bug with LigParGen
- [x] This is a feature request
I wonder whether it is possible to allow molecules with net charge larger than +/-2 to be parameterised by the …
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Are there any plans to implement O-PLS in Sklearn?
Thank you,
Keiron.
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I would like to discuss the feasibility of reading angle, dihedral and improper from files(especially LAMMPS) in this issue. Currently, there is no straightforward way to read it. I have found that th…
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I am using LigParGen Server for generating OPLS-AA Force Field parameters for small organic molecules. I have doubt regarding dihedral parameters. I am taking parameters from .key file. Energy express…
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Good morning!
Unfortanutelly, I am not able to create itp and gro file for acetonitrile. I used several variants for that, using pdb file, smile code created in draw molecula soft on your site. (CC#N…
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To better understand how atomtyping can be sped up, we should create some benchmarks. Some variables that would be worth exploring
* System size: scaling from a few hundred or thousand to hundreds …