From owner-chemistry@ccl.net Sat Sep 22 10:04:01 2007 From: "Rajarshi Guha rguha|*|indiana.edu" To: CCL Subject: CCL: PDB structures and associated ligand database Message-Id: <-35228-070921171602-17592-yc3kdNZmuIAUo7L7frxFSw/a\server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 21 Sep 2007 17:15:52 -0400 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Rajarshi Guha [rguha**indiana.edu] Hi, I am looking for a database that contains protein structures from PDB that are associated with a bound ligand. I know I could download the PDB and process the structures, but I did a literature search turned up PDB-Ligand (published in Nuc. Acids Res. http:// nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D238). However, all their email addresses are bouncing. Does anybody know how I could get in touch with the authors or whether there are alternatives to PDB-Ligand? Thanks ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- All science is either physics or stamp collecting. -- Ernest Rutherford From owner-chemistry@ccl.net Sat Sep 22 14:32:01 2007 From: "Deepangi Pandit deepangi.pandit*gmail.com" To: CCL Subject: CCL: PDB structures and associated ligand database Message-Id: <-35229-070922142227-29267-W4UIxeGd8vyG3oemz8pPTw!^!server.ccl.net> X-Original-From: "Deepangi Pandit" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 22 Sep 2007 13:21:59 -0400 MIME-Version: 1.0 Sent to CCL by: "Deepangi Pandit" [deepangi.pandit{:}gmail.com] Hi Professor: You could try http://www.bindingmoad.org/ and contacts given on the page. I am not sure if it will fulfill your requirements. THX Deepangi On 9/21/07, Rajarshi Guha rguha|*|indiana.edu wrote: > > Sent to CCL by: Rajarshi Guha [rguha**indiana.edu] > Hi, I am looking for a database that contains protein structures from > PDB that are associated with a bound ligand. I know I could download > the PDB and process the structures, but I did a literature search > turned up PDB-Ligand (published in Nuc. Acids Res. http:// > nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D238). > > However, all their email addresses are bouncing. Does anybody know > how I could get in touch with the authors or whether there are > alternatives to PDB-Ligand? > > Thanks > > ------------------------------------------------------------------- > Rajarshi Guha > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > All science is either physics or stamp collecting. > -- Ernest Rutherford> > > > -- - Deepangi From owner-chemistry@ccl.net Sat Sep 22 15:43:00 2007 From: "Huajun Fan hjfan^-^pvamu.edu" To: CCL Subject: CCL: split dimer in sdf Message-Id: <-35230-070922154143-24317-OR8sA4BaQwT9nErVHbPVbA{}server.ccl.net> X-Original-From: "Huajun Fan" Date: Sat, 22 Sep 2007 15:41:40 -0400 Sent to CCL by: "Huajun Fan" [hjfan(-)pvamu.edu] Dear CCLers I am aware of using SDF Toolkit, sdfsplit.pl and babel to split a big sdf file into smaller or even single files. Many of them using delimit symbol . However, sometimes, each sdf unit (separated by ) contains dimmer or two separated compounds, and I would like to split them too. Does anyone have any good solution to do that? Many thanks. Huajun From owner-chemistry@ccl.net Sat Sep 22 16:18:01 2007 From: "Carlos H c.hernandez!^!inbox.com" To: CCL Subject: CCL: Gaussian hyperpolarizability Message-Id: <-35231-070922115540-18138-PGNVlwhoNX3JHRtUlg/lWQ%server.ccl.net> X-Original-From: "Carlos H" Date: Sat, 22 Sep 2007 11:55:36 -0400 Sent to CCL by: "Carlos H" [c.hernandez a inbox.com] Hi all Could someone kindly explain why the hyperpolarizability values in Gaussain differ in the results and archive section? which values should be used? Example give below: results section -------------------------------------------------------- Static Hyperpolarizability: K= 1 block: 1 1 0.180271D+03 K= 2 block: 1 2 1 -0.162104D+02 2 0.115211D+02 -0.344414D+01 K= 3 block: 1 2 3 1 -0.109560D+01 2 -0.301726D+00 0.352466D+00 3 0.358494D+02 -0.134111D+02 -0.437962D-01 archive section -------------------------------------------------------- \Polar=71.4354916,-0.0213953,39.0194471,-2.4339167,0.018 6441,99.7860715\HyperPolar=-3.9069764,0.348697,-13.8830837,0.0081696,1 1.9268094,-0.2692509,35.669279,-18.2738757,-1.065183,179.5902115\PG=C0... Carlos c.hernandez _ inbox.com