From owner-chemistry@ccl.net Sat Apr 7 01:16:00 2012 From: "Alexander Bagaturyants bagaturyants#,#gmail.com" To: CCL Subject: CCL: Hydrophobic interaction - precise answer Message-Id: <-46654-120407011341-9354-mDvFBOEXVmT5zj6uaZrJJg/./server.ccl.net> X-Original-From: "Alexander Bagaturyants" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="koi8-r" Date: Sat, 7 Apr 2012 09:13:31 +0400 MIME-Version: 1.0 Sent to CCL by: "Alexander Bagaturyants" [bagaturyants|*|gmail.com] Dear professors and students! Of course, this is a useful discussion. Generally, I completely agree with John Gunn and Mihaly Mezei. What is strange, is that the student did not even carefully searched the Google. Even the first page of the search results gives you correct, physically reasonable, and complete explanations of this term. See, for example, http://www.iams.sinica.edu.tw/lab/jlli/thesis_andy/node7.html, http://en.wikipedia.org/wiki/Hydrophobic_effect, and, finally, the IUPAC definition http://goldbook.iupac.org/H02907.html. These are the first lines that you find by the request. Many good references are given in the WIKI article, and a comprehensive modern review is given by David Chandler, Interfaces and the driving force of hydrophobic assembly, Nature, vol. 437, pp. 640-647. Of course, from a physical point of view, the concept of forces, potentials, and interactions is not restricted to a pure mechanical sense, but can be considered thermodynamically. We live in a thermodynamical World, and almost all (and, might be, all) phenomena that we observe are thermodynamical phenomena. Hydrophobic interactions are a good reminder of that. Best regards Alexander Alexander A. Bagaturyants Photochemistry Center Russian Academy of Sciences ul. Novatorov 7a, b. 1 Moscow 119421 Russia Phone: +7(495)9362588 (office) +7(916)5317022 (mobile) Fax: +7(495)9361255 e-mail: sasha _ photonics.ru bagaturyants _ gmail.com > -----Original Message----- > From: owner-chemistry+sasha==photonics.ru _ ccl.net [mailto:owner- > chemistry+sasha==photonics.ru _ ccl.net] On Behalf Of Mezei, Mihaly > mihaly.mezei###mssm.edu > Sent: 07 April, 2012 01:45 > To: Alexander Bagaturyants > Subject: CCL: Hydrophobic interaction - precise answer > > > Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei,+,mssm.edu] I was about > to make this point as well. Especially since potential of men force > between two methanes obtained from explicit water simulations show > definite minima as well. > > Mihaly Mezei > > Department of Structural and Chemical Biology, Mount Sinai School of > Medicine > Voice: (212) 659-5475 Fax: (212) 849-2456 > WWW (MSSM home): > http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=000007250000 > 1497192632 > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > WWW (Department): http://atlas.physbio.mssm.edu > ____________________________________ > > From: owner-chemistry+mihaly.mezei==mssm.edu^^^ccl.net > > [owner-chemistry+mihaly.mezei==mssm.edu^^^ccl.net] on behalf of John > > Gunn jgunn]*[mailaps.org [owner-chemistry^^^ccl.net] > Sent: Friday, April 06, 2012 9:28 AM > To: Mezei, Mihaly > Subject: CCL: Hydrophobic interaction - precise answer > > Actually, people often use this to refer to an effective attraction > between non-polar solutes due to the water entropy. You can define a > potential of mean force like this: > > phi(r_1,r_2) = -kTln[ (1/Z(R))int(dR) exp(-beta*E(r_1,r_2,R)) ] - > U(r_1,r_2) > > where r_i is the position of solute i and R is the configuration of all > water molecules and E is the energy of the entire system, in other > words a pair correlation function for the solute. Note that phi=0 if > E=U(r_1,r_2)+U(R). > Of course this implies an implicit-solvent model, but it can be used as > an empirical correction for MM forcefields, often based on surface area > for the reasons you described. > > -John.> To recover the email address of the author of the message, please > change the strange characters on the top line to the _ sign. You can > also From owner-chemistry@ccl.net Sat Apr 7 10:01:01 2012 From: "VITORGE Pierre 094605 Pierre.VITORGE(!)cea.fr" To: CCL Subject: CCL:G: Visualize NLMOs from Gaussian output/checkpoint file Message-Id: <-46655-120407043013-3157-1L5tyEvjIxRplCu0C92Fiw%%server.ccl.net> X-Original-From: VITORGE Pierre 094605 Content-Language: fr-FR Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Sat, 7 Apr 2012 08:30:02 +0000 MIME-Version: 1.0 Sent to CCL by: VITORGE Pierre 094605 [Pierre.VITORGE : cea.fr] Is it also possible to visualize these orbitals with the last version of Molekel? Does Molekel 4.3 give correct results? I had some surprises when comparing orbitals plotted with Molekel 4.3 and -from gaussian cube file- with VMD. -- Pierre Vitorge Directeur de recherche CEA Laboratoire Analyse et Modelisation pour la Biologie et l Environnement, LAMBE, UMR 8587, CEA, Univ Evry, CNRS, Bd. Francois Mitterrand, Bat. Maupertuis, s 02  F-91025 Evry, France tel.01.69.47.01.40 (+33.1.69.47.01.40) pierre.vitorge[]univ-evry.fr http://www.lambe.univ-evry.fr/pvitorge http://www.vitorge.name -- Laboratoire de Radiolyse et de la Matiere Organique, LRMO (this is the new name of the lab.) CEA, DEN, Saclay, DPC, SECR, Bat.391 Pe.121 F-91191 Gif-sur-Yvette, France. tel.01.69.08.32.65 (+33.1.69.08.32.65) -----Message d'origine----- De : owner-chemistry+pierre.vitorge==cea.fr[]ccl.net [mailto:owner-chemistry+pierre.vitorge==cea.fr[]ccl.net] De la part de Jose A. Gamez jgamez#%#mpi-muelheim.mpg.de Envoyé : vendredi 6 avril 2012 13:15 À : VITORGE Pierre 094605 Objet : CCL:G: Visualize NLMOs from Gaussian output/checkpoint file Sent to CCL by: "Jose A. Gamez" [jgamez%%mpi-muelheim.mpg.de] Dear Wilhelm, Here is a small tutorial to visualise NBO related orbitals with molekel4.3 (it doesn't work with the last version). You can get molekel4.3 from: ftp://ftp.cscs.ch/out/molekel/molekel_4.3/ in the input file add: gfoldprint pop=(full,nboread) and before the last blank line of the gaussian input, add: $NBO PLOT FILE=filename $END at the end of your calculation, in addition to the output, you will also have eleven filename.[31-41] files. The NLMOs are stored in the filename.39 (you can see it in the header of the file), NBOs in filename.38 and so on. Now we have to convert the Gaussian09 output (output.log) in something understandable for molekel 4.3 (molekel.log), so just run: sed "s/Gaussian 09/Gaussian 98/" output.log | sed "s/Eigenvalues/EIGENVALUES/g" > molekel.log Open molekel, right-button click (keep pressing the button), load -> gaussian log and select molekel.log. Once you have your molecule, right-button click, load -> nbo orb (remove the filter .orb) and select filename.39. Finally, right-button click, compute -> orbital and select the orbital you want to visualise. I hope this helps. In case you have further questions, feel free to ask me. Cheers, Jose On Thursday 05 April 2012 16:39:30 you wrote: > Sent to CCL by: Wilhelm Eger [eger*o*theochem.tu-muenchen.de] > Dear all, > > In order to compare the shapes of a NLMO LP and its parent NBO in regard > to delocalization effects, I would like to extract both as a cube file > > > from a Gaussian calculation. > > I know the actual procedure consisting of: > > Run the NBO calculation with the POP=(SaveNBOs) keyword. > > Transform the resulting checkpoint file to a formatted chechkpoint file > using formchk. > > Look at the end of the calculation output file and get the right > position of the desired NBO. > > Extract the NBO with > > cubegen 0 mo=X file.fchk MOX.cube -3 h > > and all other related with > > cubegen 0 mo=Y file.fchk MOY.cube -3 h MOX.cube > > to ensure the same dimensions. > > However, if I run the calculation with POP=(SaveNLMOs), and extract the > related MO, I get exactly the same cube files as for the NBO extraction > method (e.g. diff results zero). The Gaussian output tells me also of > NBOs being stored in the checkpoint file instead of NLMOs. Besides of > 'SaveNLMOs' I tried 'SaveMixed' and 'IOP=(6/7=3)', but still the same > result. Both G03 and G09 have been used. The desired NBO and NLMO must > be different due to significant delocalization of the parent NBO into > antibonds. > > Does anybody know how to reliably extract NLMOs to cube files? > > Thanks in advance. > > Regards, > > Wilhelm -- Dr. Jose A. Gamez Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr/Germany Tel.: +49 208 306 2171http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sat Apr 7 10:47:02 2012 From: "Richard W Harper drrwharper%gmail.com" To: CCL Subject: CCL: Homology modeling of protein with more than one chain Message-Id: <-46656-120407104451-29994-/lelrDBian4OsxED/sa47A- -server.ccl.net> X-Original-From: "Richard W Harper" Date: Sat, 7 Apr 2012 10:44:47 -0400 Sent to CCL by: "Richard W Harper" [drrwharper__gmail.com] I am attempting to build a homology model of a protein with more than one chain. The only way I have discovered to accomplish this is to model the two chains independently and combine them by overlaying on the x-ray structure. Is there a better way? Thanks for helping, Dick Indiana University-Purdue University Indianapolis (IUPUI)