{"action":"closed","issue":{"url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/issues/344","labels_url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/issues/344/labels{/name}","comments_url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/issues/344/comments","events_url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/issues/344/events","html_url":"https://github.com/Electrostatics/apbs-pdb2pqr/issues/344","id":107532110,"number":344,"title":"More informative error message for CNT atoms","user":{"login":"lizutah","id":1486218,"avatar_url":"https://avatars.githubusercontent.com/u/1486218?v=3","gravatar_id":"","url":"https://api.github.com/users/lizutah","html_url":"https://github.com/lizutah","followers_url":"https://api.github.com/users/lizutah/followers","following_url":"https://api.github.com/users/lizutah/following{/other_user}","gists_url":"https://api.github.com/users/lizutah/gists{/gist_id}","starred_url":"https://api.github.com/users/lizutah/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lizutah/subscriptions","organizations_url":"https://api.github.com/users/lizutah/orgs","repos_url":"https://api.github.com/users/lizutah/repos","events_url":"https://api.github.com/users/lizutah/events{/privacy}","received_events_url":"https://api.github.com/users/lizutah/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/labels/pdb2pqr","name":"pdb2pqr","color":"5319e7"}],"state":"closed","locked":false,"assignee":{"login":"kmonson","id":2049915,"avatar_url":"https://avatars.githubusercontent.com/u/2049915?v=3","gravatar_id":"","url":"https://api.github.com/users/kmonson","html_url":"https://github.com/kmonson","followers_url":"https://api.github.com/users/kmonson/followers","following_url":"https://api.github.com/users/kmonson/following{/other_user}","gists_url":"https://api.github.com/users/kmonson/gists{/gist_id}","starred_url":"https://api.github.com/users/kmonson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kmonson/subscriptions","organizations_url":"https://api.github.com/users/kmonson/orgs","repos_url":"https://api.github.com/users/kmonson/repos","events_url":"https://api.github.com/users/kmonson/events{/privacy}","received_events_url":"https://api.github.com/users/kmonson/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/milestones/24","html_url":"https://github.com/Electrostatics/apbs-pdb2pqr/milestones/APBS%201.4.2%20release","labels_url":"https://api.github.com/repos/Electrostatics/apbs-pdb2pqr/milestones/24/labels","id":1207413,"number":24,"title":"APBS 1.4.2 release","description":"","creator":{"login":"lizutah","id":1486218,"avatar_url":"https://avatars.githubusercontent.com/u/1486218?v=3","gravatar_id":"","url":"https://api.github.com/users/lizutah","html_url":"https://github.com/lizutah","followers_url":"https://api.github.com/users/lizutah/followers","following_url":"https://api.github.com/users/lizutah/following{/other_user}","gists_url":"https://api.github.com/users/lizutah/gists{/gist_id}","starred_url":"https://api.github.com/users/lizutah/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lizutah/subscriptions","organizations_url":"https://api.github.com/users/lizutah/orgs","repos_url":"https://api.github.com/users/lizutah/repos","events_url":"https://api.github.com/users/lizutah/events{/privacy}","received_events_url":"https://api.github.com/users/lizutah/received_events","type":"User","site_admin":false},"open_issues":15,"closed_issues":15,"state":"open","created_at":"2015-07-14T17:06:34Z","updated_at":"2015-09-21T16:39:21Z","due_on":"2015-10-01T07:00:00Z","closed_at":null},"comments":0,"created_at":"2015-09-21T15:02:56Z","updated_at":"2015-09-21T16:39:21Z","closed_at":"2015-09-21T16:39:21Z","body":"Hi Kyle --\r\n\r\nCan we please make this error message more informative?\r\n\r\nThanks,\r\n\r\n--\r\nNathan Baker\r\nLaboratory Fellow\r\nComputational and Statistical Analytics Division\r\nPacific Northwest National Laboratory\r\n+1-509-375-3997\r\nhttps://goo.gl/H3X8f1\r\n\r\nBegin forwarded message:\r\n\r\nFrom: \"Baker, Nathan\" <Nathan.Baker@pnnl.gov>\r\nSubject: Re: PDB2PQR: urgent technical query\r\nDate: September 21, 2015 at 06:04:05 PDT\r\nTo: Neelanjana Sengupta <n.sengupta@ncl.res.in>\r\nCc: Asiskumar jana <ak.jana@ncl.res.in>, \"Monson, Kyle E\" <Kyle.Monson@pnnl.gov>, \"Jurrus, Elizabeth R\" <Elizabeth.Jurrus@pnnl.gov>\r\n\r\nHello --\r\n\r\nYou will not be able to parameterize your CNT with PDB2PQR because it does not have parameters for the CNT atoms -- that is what the obscure error message is trying to communicate.  You will need to construct the PQR file manually by adding the charge and radius your PDB file as described here:  http://www.poissonboltzmann.org/docs/file-format-info/\r\n\r\nSincerely,\r\n\r\n--\r\nNathan Baker\r\nLaboratory Fellow\r\nComputational and Statistical Analytics Division\r\nPacific Northwest National Laboratory\r\n+1-509-375-3997\r\nhttps://goo.gl/H3X8f1\r\n\r\nOn Sep 20, 2015, at 20:50, Neelanjana Sengupta <n.sengupta@ncl.res.in> wrote:\r\n\r\nDear Nathan,\r\n\r\nI had requested for Subscription to the mailing list two days back. Since I haven't been accepted yet, and as this request is very urgent (required for a paper revision), I am writing to you directly. Would appreciate your help very much. My graduate student, Asis, is copied on the email.\r\n\r\nWe are trying to calculate binding free energy of a protein with a carbon nanotube (CNT) using APBS and PDB2PQR. For CNT, carbon atoms are modelled as uncharged Lennard- Jones particles using aromatic SP2 carbon atoms of the CHARMM force field. Our topology file was thus build manually. But, we are not able to generate PQR file from pdb, for CNT using PDB2PQR with CHARMM package. Errors are shown below :\r\n\r\nTraceback (most recent call last):\r\n  File \"/usr/share/pdb2pqr/pdb2pqr.py\", line 65, in <module>\r\n    mainCommand(sys.argv)\r\n  File \"/usr/share/pdb2pqr/main.py\", line 619, in mainCommand\r\n    ffout = options.ffout)\r\n  File \"/usr/share/pdb2pqr/main.py\", line 284, in runPDB2PQR\r\n    myRoutines.findMissingHeavy()\r\n  File \"/usr/share/pdb2pqr/src/routines.py\", line 614, in findMissingHeavy\r\n    raise ValueError, \"No heavy atoms found!\"\r\nValueError: No heavy atoms found!\r\n\r\nI am attaching the PSF and PDB file of the CNT. Could you suggest ways to get around this problem?\r\n\r\nThanks  a lot.\r\n\r\nBest regards,\r\nNeelanjana\r\n\r\n\r\nNeelanjana Sengupta, PhD\r\nScientist, Physical Chemistry Division\r\nand\r\nAssistant Professor, AcSIR\r\nCSIR-National Chemical Laboratory\r\nDr. Homi Bhaba Road\r\nPune 411008, India\r\nPhone: +91-20-2590 2087\r\nFax: +91-20-2590 2636\r\nWebsite: \r\nhttp://academic.ncl.res.in/n.sengupta\r\n\r\n\r\n\r\n\r\n\r\nDisclaimer:\r\n\r\nThis message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx\r\n"}}