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[GROMACS tutorial](http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html )
[GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design](https://doi.org/10.1021/acs.jcim.2c0004…
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Hello, I will be conducting molecular dynamics for several protein-ligand complexes. Is it possible to calculate the interaction energy between the protein and the ligand for individual simulation ste…
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For checking:
```
PMID:1482118 | Genetics of the fission yeast Schizosaccharomyces pombe.
PMID:7011176 | Genetics of the fission yeast Schizosaccharomyces pombe.
PMID:9439701 | Identif…
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Hi,
Thank you for all the previous help.
I am having issues with the ExtendModel function. It seems like my selections for the backbone and calphas are correct, but I am continuously getting the…
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Got this strange bug I haven't seen elsewhere in which I was modelling some data in Rex and the first 101 residues to be exact, posterior estimates are identical and so giving no resolution in any of …
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- [ ] [Correlated gene modules uncovered by high-precision single-cell transcriptomics](https://www.pnas.org/doi/abs/10.1073/pnas.2206938119)
- [x] [Dynamics of single-cell protein covariation during…
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Hi,
I've been encountering an issue with antechamber recently - it seems like it really doesn't like negatively charged nitrogens. [Here is an example molecule in SDF format.](https://drive.google.…
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Not many people are using scfix with Martini3 proteins even though it improves side-chain conformations and dynamics. Perhaps it would be best to make this option default.
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Hi.
I'm new in molecular dynamics. May I ask several silly questions?
1. How to generate the input file with MDtraj format like .xct and .gro?
2. If the target protein does not have crystal stru…
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**Aim:**
This issue addresses how to apply LigGrep to filter through docked ligand poses to check that they retain key interactions with the protein that are observed in crystallographic fragment-p…