From chemistry-request%!at!%ccl.net Mon Nov 3 09:43:12 2003 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA3EgfhP018864 for ; Mon, 3 Nov 2003 09:42:41 -0500 Received: from smeagol.unb.ca (smeagol.unb.ca [131.202.3.52]) by mailserv.unb.ca (8.12.10/8.12.6) with ESMTP id hA3EgYmc019812; Mon, 3 Nov 2003 10:42:34 -0400 Received: from smeagol.unb.ca (localhost.localdomain [127.0.0.1]) by smeagol.unb.ca (8.12.8/8.12.8) with ESMTP id hA3EgYvQ005791; Mon, 3 Nov 2003 10:42:34 -0400 Received: (from apache /at\localhost) by smeagol.unb.ca (8.12.8/8.12.8/Submit) id hA3EgXnJ005788; Mon, 3 Nov 2003 10:42:33 -0400 Received: from raven.chem.unb.ca (raven.chem.unb.ca [131.202.164.46]) by webmail.unb.ca (IMP) with HTTP for ; Mon, 3 Nov 2003 10:42:33 -0400 Message-ID: <1067870553.3fa669593a9a1$at$webmail.unb.ca> Date: Mon, 3 Nov 2003 10:42:33 -0400 From: "Flight, Robert Maxwell" Reply-to: robert.flight$at$unb.ca To: Alex Sutcliffe , -: at :-unb.ca, Computational Chemistry List Subject: Re: ADL: fixing non-integral charges References: <20031103143214.GA21755 ^at^ alex> In-Reply-To: <20031103143214.GA21755 ^%at%^ alex> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.164.46 X-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: not spam (whitelisted), SpamAssassin (score=-2.4, required 5, FROM_HAS_MIXED_NUMS, IN_REP_TO, QUOTED_EMAIL_TEXT, REFERENCES, SPAM_PHRASE_00_01, USER_AGENT, USER_AGENT_IMP) X-Spam-Status: No, hits=-2.3 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_IMP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Alex, > I am trying to use autodock via adt. When I read in my ligand it > complains that the charge on the molecule is not integral and to fix > this in the written file and mentions specific residues. From the > written pdbq file an example is > > ATOM 1 N ALA A 295 76.602 58.846 18.320 1.00 15.64 -0.520 > ATOM 2 HN1 ALA A 295 76.335 59.392 19.139 1.00 0.00 0.000 > ATOM 3 HN2 ALA A 295 76.036 59.070 17.502 1.00 0.00 0.000 > ATOM 4 HN3 ALA A 295 77.509 59.124 17.946 1.00 0.00 0.000 > ATOM 5 CA ALA A 295 76.552 57.441 18.657 1.00 15.00 0.215 > ATOM 6 C ALA A 295 76.956 56.616 17.418 1.00 18.88 0.526 > ATOM 7 O ALA A 295 77.711 55.640 17.578 1.00 17.66 -0.500 > ATOM 8 CB ALA A 295 75.172 57.039 19.105 1.00 12.54 0.031 > From what you show here, I'm guessing that the alanine is at a break point in the protein (if it was continuous then the Nitrogen should have only one H like the other one you listed), you should visually check this to be sure. I have personally had a lot of trouble with partial charges on any residues that are at a break in my proteins. > ie it only has HN not HN1,2,3 and the charge on it is .248 thus giving a > net charge of 0. > > So to fix this file do I want to simply delete the extra HN lines and > change the charge from 0 to 0.248 or do I fix it some other way? Personally, I have started ignoring the message as long as residue was not near or part of the active site, and I have not noticed it making any difference in my docking results. If you really wanted, you could distribute a positive 0.248 charge evenly between the three hydrogens. That would be the safe bet, and is relatively painless if you only have to do it once. Hope this helps. Cheers, -Robert *************************** Robert Flight Master Candidate Computational Chemistry Department of Chemistry University of New Brunswick Fredericton NB, Canada E3B 6E2 e-mail: robert.flight$at$unb.ca *************************** "A computer terminal is not some clunky old television with a typewriter in front of it. It is an interface where the mind and body can connect with the universe and move bits of it about." -- Hitch Hikers Guide to the Galaxy