From owner-chemistry@ccl.net Fri Feb 18 00:26:01 2011 From: "Jan Labanowski janl##speakeasy.net" To: CCL Subject: CCL: Internet problems with CCL Message-Id: <-43978-110218002215-27885-tg5YG542XPFpq0EYTT4AdQ/./server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Fri, 18 Feb 2011 00:22:06 EST MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl%x%speakeasy.net] Dear CCL Members, You may have noticed that there are problems with accessing the CCL.NET on the internet. It is intermittent. I suspect that it has something to do with my phone lines. My FAX line is fine, the other, on which I have DSL with CCL, is noisy and my DSL modem goes up/down all the time. Of course, I reported... Using their web page at att.com on my other Internet (cable). There is no way to talk to the human at AT&T (you can only order things from a human, but you cannot talk to an "off-shore" front for a repair technician). I also like their web site: they accept 100 characters for a detailed description of the problem (I removed all the's and a's and subjects). Moreover, if you enter your phone number with hyphens, they tell you to remove the dashes, like they did not know that you can do: tel =~ s/[^0-9]//g either on the server or in the JavaScript. It always make me wonder who makes those web sites for the big guys... Highschool kids? My son used to make better pages in highschool, though. After listening to music for 2 (two) hours on the speakerphone, interruped with "Your call is very important to "ass". All our agents are "ass"-isting other customers. The next available agent will be with you shortly", I had to hang up. It seems that "they do more with less" like most other companies who dumped people on the streets. Sorry folks... There is not much more I can do... You have to bear with me... Jan -- Jan Labanowski jkl#ccl.net From owner-chemistry@ccl.net Fri Feb 18 04:10:00 2011 From: "quartarolo++unical.it" To: CCL Subject: CCL:G: calculated emission spectra help Message-Id: <-43979-110218033734-12915-Qi57K9xbAC+fi1kKRkRLfw[*]server.ccl.net> X-Original-From: quartarolo(~)unical.it Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 18 Feb 2011 09:37:19 +0100 MIME-Version: 1.0 Sent to CCL by: quartarolo^-^unical.it Hi, for an example of emission calculation including solvent effects, you can look directly at: http://www.gaussian.com/g_tech/g_ur/k_scrf.htm domenico Chemistry Dept, UNICAL (Italy) Quoting "Bradley Kenneth Welch bwelch5_-_slu.edu" : > > Sent to CCL by: "Bradley Kenneth Welch" [bwelch5:_:slu.edu] > Deal CCL readers, > > > I'm having trouble calculating the emission spectra for some > metallocarboranes in the gas phase with Gaussian 09. I know for the > absorption part of the spectra you want to run a single point with > TDDFT on the ground state equilibrium geometry. I am at a loss on > how I would calculate the emission part of the spectra. > > > Bradley Welch > Saint Louis University > St.Louis, MO > Room 218> > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Fri Feb 18 10:27:00 2011 From: "Heribert Reis hreis-,-eie.gr" To: CCL Subject: CCL: Problems with adding hydrogens Message-Id: <-43980-110218102319-12725-6l8OPyqulokhrBtE7fwGfg:_:server.ccl.net> X-Original-From: Heribert Reis Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Fri, 18 Feb 2011 17:12:33 +0200 Mime-Version: 1.0 Sent to CCL by: Heribert Reis [hreis.:.eie.gr] Hi I need to add Hydrogens to a large number of pdb-files, which all contain the same molecules in different configurations (the results of molecular simulation run with implicit hydrogens). I use babel with the 'add hydrogen' option, which usually works fine, but sometimes interprets a -C-C- group as -CH=CH-, instead of -CH2-CH2- group, and adds only 2H instead of 4. Is there a way to correct this? For example, can I tell babel explicitly to treat a C-atom as sp3, and not as sp2? Thanks for any suggestions, Heribert From owner-chemistry@ccl.net Fri Feb 18 12:06:00 2011 From: "Geoffrey Hutchison geoffh||pitt.edu" To: CCL Subject: CCL: Problems with adding hydrogens Message-Id: <-43981-110218115144-26076-qNX4UiZ3bU6KY/VwEzfYwA * server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Fri, 18 Feb 2011 11:51:18 -0500 MIME-version: 1.0 (Apple Message framework v1082) Sent to CCL by: Geoffrey Hutchison [geoffh .. pitt.edu] > I need to add Hydrogens to a large number of pdb-files, which all > contain the same molecules in different configurations (the results of > molecular simulation run with implicit hydrogens). I use babel with the > 'add hydrogen' option, which usually works fine, b Well, you posted this to the openbabel mailing list and got an answer there too. Unless it's really a file from the Protein Data Bank (with actual atom names), PDB files are not a good interchange format. On Feb 18, 2011, at 10:14 AM, Pascal Muller wrote: > pdb doesn't contains information about bond type... Seems that the > simulation shortened the bond... As far as I know, the only way to > determine bond type in a pdb file is the bond length. > >> and >> adds only 2H instead of 4. Is there a way to correct this? For example, >> can I tell babel explicitly to treat a C-atom as sp3, and not as sp2? > > Does your software generate output in e.g. mol2? The software should > know the atom/bond type, isn't it? > Why not include hydrogens before the simulation? I agree completely with Pascal. Try mol2 or mol/sdf if you want to retain atom types. Otherwise Open Babel has to "perceive" bond orders and without hydrogens to complete the valence, we have to base hybridization on bond lengths and angles. It's good, but not fool-proof. Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh(_)pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Fri Feb 18 12:45:00 2011 From: "carlos franca carfranca120*gmail.com" To: CCL Subject: CCL: Problems with adding hydrogens Message-Id: <-43982-110218123454-30974-52JxvaxB5nO8We46dz3AnA^^server.ccl.net> X-Original-From: carlos franca Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Fri, 18 Feb 2011 14:34:29 -0300 MIME-Version: 1.0 Sent to CCL by: carlos franca [carfranca120+/-gmail.com] heribert, you can explore the next page of PyBabel, there are two forms for adding H with module addh http://mgltools.scripps.edu/api/PyBabel/PyBabel.addh-module.html El 18/02/11 12:12, Heribert Reis hreis-,-eie.gr escribió: > Sent to CCL by: Heribert Reis [hreis.:.eie.gr] > Hi > > I need to add Hydrogens to a large number of pdb-files, which all > contain the same molecules in different configurations (the results of > molecular simulation run with implicit hydrogens). I use babel with the > 'add hydrogen' option, which usually works fine, but sometimes > interprets a -C-C- group as -CH=CH-, instead of -CH2-CH2- group, and > adds only 2H instead of 4. Is there a way to correct this? For example, > can I tell babel explicitly to treat a C-atom as sp3, and not as sp2? > > Thanks for any suggestions, > Heribert> > > From owner-chemistry@ccl.net Fri Feb 18 16:06:00 2011 From: "Jim Kress ccl_nospam*_*kressworks.com" To: CCL Subject: CCL:G: calculated emission spectra help Message-Id: <-43983-110218151621-2018-xh3hOv/sIgYgiUQ1f7EwCQ[#]server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 18 Feb 2011 15:16:13 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam|-|kressworks.com] Try ORCA. It's easier to use, faster and has an integrated spectrum methodology that's more accurate and has better support. http://www.thch.uni-bonn.de/tc/orca/ Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com=-=ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com=-=ccl.net] On Behalf Of > quartarolo++unical.it > Sent: Friday, February 18, 2011 3:37 AM > To: Kress, Jim > Subject: CCL:G: calculated emission spectra help > > > Sent to CCL by: quartarolo^-^unical.it > Hi, > for an example of emission calculation including solvent effects, you > can look directly at: > http://www.gaussian.com/g_tech/g_ur/k_scrf.htm > > domenico > > Chemistry Dept, UNICAL (Italy) > > > > Quoting "Bradley Kenneth Welch bwelch5_-_slu.edu" chemistry..ccl.net>: > > > > > Sent to CCL by: "Bradley Kenneth Welch" [bwelch5:_:slu.edu] > > Deal CCL readers, > > > > > > I'm having trouble calculating the emission spectra for some > > metallocarboranes in the gas phase with Gaussian 09. I know for the > > absorption part of the spectra you want to run a single point with > > TDDFT on the ground state equilibrium geometry. I am at a loss on > > how I would calculate the emission part of the spectra. > > > > > > Bradley Welch > > Saint Louis University > > St.Louis, MO > > Room 218> > > > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program.> To recover the email address of the author of the message, please > change> From owner-chemistry@ccl.net Fri Feb 18 16:40:00 2011 From: "Wang, Yixuan yixuan.wang],[asurams.edu" To: CCL Subject: CCL: IP and EA for infinite systems Message-Id: <-43984-110218154029-28063-bfSCWtrYekcgV+qsL9UUnw|server.ccl.net> X-Original-From: "Wang, Yixuan" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 18 Feb 2011 20:40:21 +0000 MIME-Version: 1.0 Sent to CCL by: "Wang, Yixuan" [yixuan.wang{=}asurams.edu] Dear All, If you are familiar with, could you talk a little about the procedures to calculate IP ( work function) and EA for infinite systems with DMOl3, or other software implementing periodic DFT? Thanks in advance Yixuan Wang, Ph.D Associate Professor Department of Chemistry Albany State University Albany, GA 31705 Tel: 229-430-7843