{"id":37617654,"url":"https://github.com/bio-phys/ff-mg-ca-nucleicacids","last_synced_at":"2026-01-16T10:33:33.196Z","repository":{"id":38355299,"uuid":"331366540","full_name":"bio-phys/ff-Mg-Ca-NucleicAcids","owner":"bio-phys","description":"Extension for the interactions with DNA and RNA of our previously bulk-optimized force field parameters (https://doi.org/10.1063/1.5017694) ","archived":false,"fork":false,"pushed_at":"2022-06-23T07:25:35.000Z","size":1577,"stargazers_count":0,"open_issues_count":1,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-09T16:20:42.354Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bio-phys.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-01-20T16:34:16.000Z","updated_at":"2022-06-23T07:25:38.000Z","dependencies_parsed_at":"2022-08-25T01:31:28.437Z","dependency_job_id":null,"html_url":"https://github.com/bio-phys/ff-Mg-Ca-NucleicAcids","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/bio-phys/ff-Mg-Ca-NucleicAcids","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fff-Mg-Ca-NucleicAcids","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fff-Mg-Ca-NucleicAcids/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fff-Mg-Ca-NucleicAcids/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fff-Mg-Ca-NucleicAcids/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bio-phys","download_url":"https://codeload.github.com/bio-phys/ff-Mg-Ca-NucleicAcids/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bio-phys%2Fff-Mg-Ca-NucleicAcids/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478050,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T06:30:42.265Z","status":"ssl_error","status_checked_at":"2026-01-16T06:30:16.248Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-01-16T10:33:33.122Z","updated_at":"2026-01-16T10:33:33.182Z","avatar_url":"https://github.com/bio-phys.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# ff-Mg-Ca-NucleicAcids\n(https://aip.scitation.org/doi/full/10.1063/5.0048113) Extension for the interactions with DNA and RNA of our previously bulk-optimized force field parameters (https://doi.org/10.1063/1.5017694) \n\n## Introduction\n******************\nPreviously, we have developed force field parameters for the metal cations in combination with the TIP3P water model.\nHere, we extend the applicability of the parameters for Mg2+ and Ca2+  to correctly describe their interactions with DNA and RNA in biomolecular simulations by including experimental binding affinities toward the phosphate oxygen. \n\nThe improved parameters improved the agreement of the binding affinities and resulted in an improvement of structural properties of the bound ions in the experimental structures.\n\nThe advantage of the current approach is that it leaves the ion-water and ion-ion interactions unchanged and can therefore be transferred easily to other ion binding sites on biomolecules.\n\n## Quick start guide\n******************\nOur parameters are optimized for the TIP3P water model.\nThe parameters work in combination with RNA (Amber99sb-ildn* + parmbsc0 +a χ0L3)  and DNA (Amber99sb-ildn* + parmbsc1) force fields .\nFor Mg2+ and Ca2+ interacting with the atom type  O2, the Lorentz-Berthelot combination rule is modified.\nNote that we have chosen unique names for the optimized parameters to avoid errors in overwriting atom names:\n* CXY - Cl\n* Mg2 - MG\n* Ca2 - CA\n\n\n## Example: Double stranded DNA (PDB-id: 477D) in 0.06 M of CaCl2\n******************\nThe folder example_477d contains all files for an MD simulation with GROMACS of a 12-bp double-stranded DNA (PDB-id: 477D) with the optimized parameters.\nInitial coordinates are given in 477d.gro.\n\n## Citation\n******************\nIf you use our optimized parameters for Mg2+ and Ca2+ optimized for the interactions with nucleic acids, please cite:\n\nS. Cruz-León, K. K. Grotz  and N. Schwierz, J. Chem. Phys. **154**, 171102 (2021)\nhttps://aip.scitation.org/doi/full/10.1063/5.0048113\n\n\nImplementation has been tested by Sergio Cruz-León and Kara K. Grotz.\nUSE AT YOUR OWN RISK!!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio-phys%2Fff-mg-ca-nucleicacids","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbio-phys%2Fff-mg-ca-nucleicacids","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbio-phys%2Fff-mg-ca-nucleicacids/lists"}