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Hi!
I find that the parameters of `` in force field files have the unit of `kcal`. That seems inconsistent with the default setting of openmm units described in [this page](http://docs.openmm.org/l…
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Hi everyone,
I am working on hydrated docking with large ligand library using same script. Hydrated docking works fine for some ligands that do not contain OA or HD atom type.
I get "ERROR: the ma…
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Hello,
I defined dihedrals for RNA for residue-2 as per the documentation. I do have 20 or more residues to include and total 6 angles for each residue that I suppose to define.
d = Dihedral…
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Add available SARS-CoV-2 data to the pipeline
- [x] @alexsign to produce GPI file
- [x] add to NEO (change config line in Makefile)
- [x] @alexsign to produce GAF/GPAD (this will be mostly interp…
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what does PROT_IDX_LIST indicate in the salt bridge?
Also, the format is a little strange. For other records, the first 6 columns remain the same and in the salt bridge, the PROT_IDX_LIST came in....…
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I don't know if it's useful but here's the list of publications with structures in PDB but don't have an APPROVED session:
```
PMID:10801440
PMID:11273706
PMID:11709168
PMID:1…
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[iPBSA_byEvenilton.zip](https://github.com/sahakyanhk/iPBSA/files/10169873/iPBSA_byEvenilton.zip)
Myself and other colleagues tried to use the iPBSA.sh but without success.
We managed to edit the …
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I tried multiple different RNA pdbs and all throw the same error `ValueError: No template found for residue 1 (C). The set of atoms matches C5, but the bonds are different. Perhaps the chain is miss…
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### Problem
I'm having trouble creating a RNA system with `espaloma`. I want to apply the espaloma force field to the RNA and treat all other components (water and ions) with the traditional force fi…
kntkb updated
2 years ago