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Hello,
I have been using LigParGen to generate OPLS parameters for an organic catalyst I've been using for research, and haven't had any issues, it has been working well. I've been submitting pdb…
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Hi, Can any one tell me the md analysis syntax to pick every third CA atom. For example in VMD this command is (residue % 3 == 1) and (name CA)
### Currently version of MDAnalysis: 0.16
(run `pyth…
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Is it not very surprising that the absolute free energies seem to be more reproducible than the relative free energies? I would expect the opposite. Why is it so?
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Feature request
Hello LigPArGen Users and @leelasd
I am trying to generate some OPLS parameters for my structure. Yes. there are two residues quite right but why can't LigPArGen provide the pa…
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- [x] I believe this to be a bug with LigParGen
## Issue Information
Software name & Version : g
Method:
## Expected Behavior
## Actual Behavior
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Hi, I want to generate parameter for attached three ligands: MDA, MDB, and MDC. However, Unknown error was reported... Would you help me fix this ?
Thanks !
[MDA.pdb.gz](https://github.com/lee…
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Within a force field XML file, torsions (and I'm pretty sure bonds and angles as well) can be defined using either "class" notation, e.g.
``
or "type" notation, e.g.
``
The practical use of havi…
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Dear Developers,
I have tried to get the OPLS parameters for tannic acid, but it showed unknown errors. A couple of structures optimized with semi-empirical methods were tested. The molecule has ze…
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- [ ] I believe this to be a bug with LigParGen
- [X] This is a feature request
## Issue Information
Software name & Version :
Method:
## Expected Behavior
## Actual Behavior
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Hi there,
I've been using your oplsda code for a while (because it is awesome!) but suddenly I am getting this error when I try and load the source code at the start.
source("http://pastebin.c…