Coarse-grain trajectory of SARS-CoV2 Main Protease with SIRAH force field

[PabloGGaray]

Description

Trajectory of a 15 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Main protease in its APO form. Created with the SIRAH force field.

Status

• YAML file for each piece of data
• Ready to go

[PabloGGaray]

Hi, I can't find where is the error in the "Schema Validation". I think that the descriptions in the "Details" point to the "references" but I don't understand where is the problem.

[Lnaden]

I think this is a problem with YAML interpreting the : in the reference as a dictionary mapping instead of one long string. Wrap each one of the reference list items in quotes, that should fix it.

[PabloGGaray]

This looks good and could be merged if you don't see a big error in the file.

Another question, this simulation, and others, that I going to be loading the entrances, were made using the structure from the PDB. In order to add the model tag, do I have to add a description of the PDB entry in the models directory? This is not necessary now but could be useful to make finding data easier.

[Lnaden]

The file looks fine.

We prefer you have structures and models referenced in the entries added to the Hub as well. Having those auto-link any simulations you add to the relevant structures and models. We're happy to help you fill in those gaps if you have any questions about them.

We do distinguish between the terms.

• structures are experimentally resolved entries, which also included most everything in the PDB
• models are derived and/or integrated structures from multiple data sources prepared for different tasks such as docking, FEP, virtual screening, etc. Effectively ready to go constructed molecular systems which can be used as inputs for myriad scientific research techniques.

simulations entries require at least one structure, but can also have any number of models as references.