{"id":19107930,"url":"https://github.com/haschka/pdb-nma-analysis","last_synced_at":"2026-05-30T13:30:16.946Z","repository":{"id":48519873,"uuid":"516927594","full_name":"haschka/pdb-nma-analysis","owner":"haschka","description":"A tool to perform quick normal mode analysis on a PDB file using Tirion's model.","archived":false,"fork":false,"pushed_at":"2022-10-11T09:29:53.000Z","size":28,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-03T03:20:29.498Z","etag":null,"topics":["normal-mode-analysis","normal-modes","pdb","pdb-files","sse2","ssse3","structural-biology","unix-tools"],"latest_commit_sha":null,"homepage":"","language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/haschka.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2022-07-23T01:21:01.000Z","updated_at":"2024-08-12T15:08:52.000Z","dependencies_parsed_at":"2023-01-19T20:45:56.216Z","dependency_job_id":null,"html_url":"https://github.com/haschka/pdb-nma-analysis","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fpdb-nma-analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fpdb-nma-analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fpdb-nma-analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fpdb-nma-analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/haschka","download_url":"https://codeload.github.com/haschka/pdb-nma-analysis/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240163494,"owners_count":19758023,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["normal-mode-analysis","normal-modes","pdb","pdb-files","sse2","ssse3","structural-biology","unix-tools"],"created_at":"2024-11-09T04:14:26.712Z","updated_at":"2026-05-30T13:30:16.877Z","avatar_url":"https://github.com/haschka.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pdb-nma-analysis\n\n(c) Thomas Haschka 2009-2022\n\nA tool to perform quick normal mode analysis on a PDB file\naccording to the method first proposed by\n[Tirion et al.](https://doi.org/10.1006/jmbi.1993.1135).\n\nPlease cite: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6888913.svg)](https://doi.org/10.5281/zenodo.6888913)\n\nThis tool now has a youtube tutorial: [https://youtu.be/jUBWMLQYkKk](https://youtu.be/jUBWMLQYkKk)\n\n### Compiling the Program\n\nThe program was almost completely ( by exercise ) \nwritten using the SSE2 + SSSE3 intrinsics, and as \nsuch requires an intel/amd processor supporting these \ninstructions to work. Anything built after 2008 basically\nshould do it.\n\nThe program further needs the lapack libraries. On \na contemporary Debian Based system you should be able to obtain\nall requirements using:\n```\nsudo apt-get install build-essential liblapack-dev\n```\nYou can then compile the program:\n```\ngcc -O2 -march=native nma-double.c -o nma -lm -llapack\n```\nobtaining the nma binary.\n\n### Performing Normal Mode Analysis\n\nThe nma tool is pretty self explanatory. Its arguments are:\n```\nfile: pdb file \n   k: spring constant in atom - atom interaction potential \n cut: Cutoff of atom - atom interaction in Angstr. \nnmax: highest mode to be visualized. nmax has to satisfy \n       7 \u003c nmax \u003c 100\n```\n\nin example if you download the PDB file \n[1uqq](https://files.rcsb.org/download/1QUU.pdb)\nyou may perform nma analysis in typing:\n```\n./nma 1quu.pdb pdb 0.5 15 9\n```\nwhich should yield the files:\n```\n7-mode.xyz\n8-mode.xyz\n9-mode.xyz\neigenvalues\n```\nThe eigenvalues give you an idea of how much each\nmode should get occupied as the protein gets excited.\nEach mode can be visualized for instance with \n[VMD](https://www.ks.uiuc.edu/Research/vmd/)\nusing the Van der Waals representation\nin this program you might get nice movies of each mode. \n\n### History\nThe program was in its original form written in 2009 as part of Thomas Haschka's \nMaster Theses\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhaschka%2Fpdb-nma-analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhaschka%2Fpdb-nma-analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhaschka%2Fpdb-nma-analysis/lists"}