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template.toml
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template.toml
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replicates = { }
ligands = [ ]
solvents = [ ]
[initial]
description = "<<df_organism>>; <<df_protein_name>>"
date = "<<today>>"
lead_contributor_orcid = "<<df_orcid>>"
external_link = "https://www.dsimb.inserm.fr/ATLAS/database/ATLAS/<<df_PDB>>/<<df_PDB>>.html"
[water]
is_present = false
water_density_units = "g/m^3"
[[proteins]]
molecule_id_type = "Uniprot"
molecule_id = "<<df_UniProt>>"
[software]
name = "GROMACS"
version = "v2019.4"
[forcefield]
forcefield = "CHARMM36m"
[[papers]]
title = "ATLAS: protein flexibility description from atomistic molecular dynamics simulations"
authors = "Yann Vander Meersche, Gabriel Cretin, Aria Gheeraert, Jean-Christophe Gelly, Tatiana Galochkina"
journal = "Nucleic Acids Research"
year = 2_023
volume = 52
number = "D1"
pages = "D384–D392"
doi = "10.1093/nar/gkad1084"
[[contributors]]
name = "Yann Vander Meersche"
orcid = "0000-0002-6680-8104"
institution = "Université Paris Cité"
[[contributors]]
name = "Gabriel Cretin"
orcid = "0000-0002-3522-7083"
institution = "Université Paris Cité"
[[contributors]]
name = "Aria Gheeraert"
orcid = "0000-0001-7493-8702"
institution = "Université Paris Cité"
[[contributors]]
name = "Jean-Christophe Gelly"
orcid = "0000-0001-5138-361X"
email = "jean-christophe.gelly@u-paris.fr"
institution = "Université Paris Cité"
[[contributors]]
name = "Tatiana Galochkina"
orcid = "0000-0002-3608-5208"
email = "tatiana.galochkina@u-paris.fr"
institution = "Université Paris Cité"
[required_files]
trajectory_file_name = "<<df_PDB_prod>>.xtc"
structure_file_name = "<<df_PDB_prod>>.tpr"
topology_file_name = "<<df_PDB_prod>>.tpr"
[[additional_files]]
additional_file_type = "Checkpoint"
additional_file_name = "<<df_PDB_prod>>.cpt"
additional_file_description = "Last GROMACS checkpoint of the simulation"
[[additional_files]]
additional_file_type = "Structure"
additional_file_name = "<<df_PDB>>_prod_start.gro"
additional_file_description = "GROMACS structure file of the 1st MD frame (after minimisation)"
[[additional_files]]
additional_file_type = "Structure"
additional_file_name = "<<df_PDB_prod>>_end.gro"
additional_file_description = "GROMACS structure file of the last MD frame of each replicate for easy MD prolongation"
[[additional_files]]
additional_file_type = "Topology"
additional_file_name = "<<df_PDB>>.top"
additional_file_description = "GROMACS topology file"