From owner-chemistry@ccl.net Mon Aug 18 11:51:01 2008 From: "D dean ddean86 _ gmail.com" To: CCL Subject: CCL: Scaffolds for CoMFA contour plots Message-Id: <-37574-080818103010-18496-CKS0VqUfz2aLyMMKMN6vvw]^[server.ccl.net> X-Original-From: "D dean" Date: Mon, 18 Aug 2008 10:30:06 -0400 Sent to CCL by: "D dean" [ddean86*|*gmail.com] Hello, I had performed a 3D-QSAR analysis and got favorable electropositive (blue) and electronegative (red) contour maps. I am interested to know if there are a list of scaffolds which I can use for substituting near favorable electropositive and favorable electronegative contour regions. Most of the 3D-QSAR paper just say favorable regions, or just suggest carbonyl group near electronegative and free amino group near electropositive regions. If anyone can suggest a listing of such scaffolds which I can try it will be very heplpful to me and maybe also helpful to other beginners. Thank you for your time. Best regards, DD From owner-chemistry@ccl.net Mon Aug 18 12:26:00 2008 From: "Yann Tambouret yannpaul=-=chem.bu.edu" To: CCL Subject: CCL:G: intrinsic reaction coordinate Message-Id: <-37575-080818115928-29281-AYvsoL/LYXZJFtwM9modyA]~[server.ccl.net> X-Original-From: Yann Tambouret Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 18 Aug 2008 11:27:48 -0400 MIME-Version: 1.0 Sent to CCL by: Yann Tambouret [yannpaul^chem.bu.edu] Hi, I'm trying to perform an IRC calculation in Gaussian 03. I have several issues/questions with the method: 1) Using the 'CalcFC' option, the path is followed, but eventually, the optimization routine falls into a repetitive loop of over and under shooting the minimized point along the path, so the run never converges. The loops are about 3-4 steps, and these four or so steps are exactly repeated over and over. 2) Using the 'CalcAll' option, this happens much more quickly, ie fewer points along the path are successfully converged before the routine fails. 3) Adding the 'VeryTight' and 'MaxStep=10' keywords seem to affect the overlay options and settings (just as much as they would be if the 'IOp' keyword is used), but no effect is seen in the IRC blocks of the log file. It seems the IRC routine ignores these options. 4) Can anyone offer advice on or compare the IRC method vs. the 'Path' option of the OPT method? Has anyone had more success with one or the other? Is one more cost effective? Any help clarifying the above issues will be greatly appreciated. Thanks, Yann Here is my input file. I'm using a small basis set for testing reasons. #P RB3LYP 4-31G IRC=(CalcFC,MaxPoints=20,MaxStep=10,VeryTight) ts struct 0 1 C 0.22654935 -2.08650271 0.00000000 C 1.55591580 -1.66876493 0.00000000 C 2.06556137 -0.37185267 0.00000000 C 1.38237380 0.83444750 0.00000000 Cl 2.42537013 2.33167952 0.00000000 C -0.92904135 -1.32065973 0.00000000 C -1.07451756 0.06423880 0.00000000 C 0.01103280 1.07637953 0.00000000 O -0.52974628 2.26627836 0.00000000 Cl -2.49552154 -2.25644010 0.00000000 O -2.22370216 0.68687513 0.00000000 H 0.06322275 -3.15775934 0.00000000 H -1.71086143 1.83494863 0.00000000 H 2.29494012 -2.46138999 0.00000000 H 3.14561470 -0.28381211 0.00000000 From owner-chemistry@ccl.net Mon Aug 18 16:11:00 2008 From: "Deepangi Pandit deepangi.pandit{}gmail.com" To: CCL Subject: CCL: Scaffolds for CoMFA contour plots Message-Id: <-37576-080818145856-23144-YFhVYmupf9miDiQXlN/oKA,+,server.ccl.net> X-Original-From: "Deepangi Pandit" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 18 Aug 2008 13:58:23 -0400 MIME-Version: 1.0 Sent to CCL by: "Deepangi Pandit" [deepangi.pandit]*[gmail.com] Hi DD, I am not sure if you have tried this or looking for similar stuff but if you are using SYBYL there is an option for QSAR Optimization via option optimize QSAR. I do not remember the exact menu location but please search Tripos Bookshelf for QSAR optimization or optimize QSAR. I think there is also a tutorial about the same. Deepa On Mon, Aug 18, 2008 at 10:30 AM, D dean ddean86 _ gmail.com wrote: > > Sent to CCL by: "D dean" [ddean86*|*gmail.com] > Hello, > > I had performed a 3D-QSAR analysis and got favorable electropositive (blue) and electronegative (red) contour maps. > > I am interested to know if there are a list of scaffolds which I can use for substituting near favorable electropositive and favorable electronegative contour regions. > > Most of the 3D-QSAR paper just say favorable regions, or just suggest carbonyl group near electronegative and free amino group near electropositive regions. > > If anyone can suggest a listing of such scaffolds which I can try it will be very heplpful to me and maybe also helpful to other beginners. > > Thank you for your time. > > Best regards, > > DD> > > From owner-chemistry@ccl.net Mon Aug 18 19:18:01 2008 From: "Scott Dixon scott- -daylight.com" To: CCL Subject: CCL: New GPCR Structure - Critical Assessment of GPCR Modeling and Docking 2008 Message-Id: <-37577-080818190535-30117-q+WUQD2h2q2VMdhuJYhQXA=server.ccl.net> X-Original-From: Scott Dixon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Mon, 18 Aug 2008 15:32:33 -0700 Mime-Version: 1.0 (Apple Message framework v926) Sent to CCL by: Scott Dixon [scott-*-daylight.com] Dear Colleagues, There is considerable discussion as to the current state of GPCR modeling progress, particularly in terms of docking of agonists and antagonists, as well as how fine the experimental structural coverage is needed for more reliable modeling/docking experiments. We have therefore initiated a community assessment to evaluate the current status and uncover new areas of needed investigation and development in GPCR modeling and docking based on a recently determined structure. This assessment is similar in fashion to CASP and CAPRI which continue to be critically important in evaluating the progress on de novo protein structure and protein-protein predictions. If you are interested in participating in this community project (and we hope you will be), please visit the website: http://jcimpt.scripps.edu/GPCRDock/default.aspx . Information will be sent by August 25th, with models due September 25th, 2008. Thank you for considering this opportunity and helping the scientific community evaluate where the field is at. Please forward this announcement on to any colleagues you think will be interested in participating. Sincerely, Charlie Brooks Scott Dixon John Moult Raymond Stevens