{"action":"created","issue":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/446","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/446/labels{/name}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/446/comments","events_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/446/events","html_url":"https://github.com/MDAnalysis/mdanalysis/issues/446","id":108186817,"number":446,"title":"PDB read, failed to construct topology for big index number (>99999) ","user":{"login":"alejob","id":8570681,"avatar_url":"https://avatars.githubusercontent.com/u/8570681?v=3","gravatar_id":"","url":"https://api.github.com/users/alejob","html_url":"https://github.com/alejob","followers_url":"https://api.github.com/users/alejob/followers","following_url":"https://api.github.com/users/alejob/following{/other_user}","gists_url":"https://api.github.com/users/alejob/gists{/gist_id}","starred_url":"https://api.github.com/users/alejob/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alejob/subscriptions","organizations_url":"https://api.github.com/users/alejob/orgs","repos_url":"https://api.github.com/users/alejob/repos","events_url":"https://api.github.com/users/alejob/events{/privacy}","received_events_url":"https://api.github.com/users/alejob/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/labels/Format-PDB","name":"Format-PDB","color":"006b75"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-09-24T18:25:35Z","updated_at":"2015-09-24T19:22:39Z","closed_at":null,"body":"When I load the universe in this way:\r\n\r\n```python\r\nuniverse = MDAnalysis.Universe(\"step5_assembly.pdb\", \"../WT_run1_1000_1ps.dcd\") \r\n```\r\nI have the next error:\r\n\r\n*File \"/usr/local/lib/python2.7/dist-packages/MDAnalysis/core/AtomGroup.py\", line 3705, in __init__\r\n    \"Error: {2}\".format(self.filename, parser, err))\r\nValueError: Failed to construct topology from file step5_assembly.pdb with parser <class 'MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser'> \r\nError: invalid literal for int() with base 10: '*****'*\r\n\r\n I have more than 100000 atoms, so after the 99999 index, its appear the *****, here is the part of the pdb:\r\n\r\n```\r\n...\r\nATOM  99998  H2  TIP3 2390      64.326  44.891  14.267  1.00  0.00      TIP3\r\nATOM  99999  OH2 TIP3 2391      67.275  48.893  23.568  1.00  0.00      TIP3\r\nATOM  *****  H1  TIP3 2391      66.641  48.181  23.485  1.00  0.00      TIP3\r\nATOM  *****  H2  TIP3 2391      66.986  49.547  22.931  1.00  0.00      TIP3\r\nATOM  *****  OH2 TIP3 2392      60.459  51.771  21.399  1.00  0.00      TIP3\r\n...\r\n```\r\n\r\nMaybe a solution could be to create an extension similar to XPDB (that read 5-digit residue numbers ), or like Oliver suggest,  ignore the atom number.\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/comments/143024705","html_url":"https://github.com/MDAnalysis/mdanalysis/issues/446#issuecomment-143024705","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/446","id":143024705,"user":{"login":"alejob","id":8570681,"avatar_url":"https://avatars.githubusercontent.com/u/8570681?v=3","gravatar_id":"","url":"https://api.github.com/users/alejob","html_url":"https://github.com/alejob","followers_url":"https://api.github.com/users/alejob/followers","following_url":"https://api.github.com/users/alejob/following{/other_user}","gists_url":"https://api.github.com/users/alejob/gists{/gist_id}","starred_url":"https://api.github.com/users/alejob/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alejob/subscriptions","organizations_url":"https://api.github.com/users/alejob/orgs","repos_url":"https://api.github.com/users/alejob/repos","events_url":"https://api.github.com/users/alejob/events{/privacy}","received_events_url":"https://api.github.com/users/alejob/received_events","type":"User","site_admin":false},"created_at":"2015-09-24T19:22:39Z","updated_at":"2015-09-24T19:22:39Z","body":"I try your suggestion, ```permissive=True```, but I still have the same problem. "}}