From owner-chemistry@ccl.net Wed Apr 3 08:02:00 2013 From: "sobereva sobjubao_-_yahoo.com.cn" To: CCL Subject: CCL:G: Electron Density cubic grid generation Message-Id: <-48516-130403014312-4000-kHKz/hCuuhajBimYrcL+Og[a]server.ccl.net> X-Original-From: sobereva Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 3 Apr 2013 13:42:56 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: sobereva [sobjubao\a/yahoo.com.cn] Hi, Please have a try Multiwfn (http://multiwfn.codeplex.com). You can use either .fch or .wfn/.wfx file generated by Gaussian as input file for generating cube file of electron density. This program provides rather flexible ways to set up grid. For example, to generate the cube file of electron density for H2O.wfn, after booting up Multiwfn you only need to input following commands (the texts after the double slashes are comments): E:\H2O.wfn // The file path 5 // Main function 5 1 // Electron density 3 // There will be about 1728000 grids in total, and the grid spacings in X,Y,Z are exactly identical, namely cubic grid. You can also choose other options to set up the grid, especially by option 4, you can directly specify the grid spacings in X,Y,Z manually 2 // Export the grid data to density.cub in current folder For more about generating grid data in Multiwfn, please check Section 3.6 of the manual and the examples given in Section 4.5. Tian Lu --- On Wed, 4/3/13, Gabriel Aires Urquiza Carvalho gabrielcarvalho%quimica.ufpb.br wrote: > From: Gabriel Aires Urquiza Carvalho gabrielcarvalho%quimica.ufpb.br > Subject: CCL:G: Electron Density cubic grid generation > To: "Lu, Tian " > Date: Wednesday, April 3, 2013, 2:37 AM > > Sent to CCL by: "Gabriel Aires Urquiza Carvalho" > [gabrielcarvalho**quimica.ufpb.br] > Dear CCL subscribers, > > > Is there any way I could get volumetric data of electron > density in the form > of a cubic voxelized grid? I have tried the gaussian > "cubegen" utility but it > doesn't neccessarily generates cubic grids, and I need those > to be cubic > because the other programs I'm using for my analysis can > only cubic binary > inputs and I'd rather not go through rewritting their code > unless I really > have to. > > It doesn't have to write the voxels in binary, I can convert > them to a binary > stream as an extra step in the process by writing a minor > Fortran utility, I > just need something to generate the voxels for me, in a > cubic arrangement. > > Thanks in advance! > > > Gabriel Aires Urquiza Carvalho > > gabrielcarvalho#,#quimica.ufpb.br > Programa de Ps-Graduao em Qumica > Departamento de Qumica > Universidade Federal da Paraba - Brazil > > > > -= This is automatically added to each message by the > mailing script =- > 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> > E-mail to subscribers: CHEMISTRY!^!ccl.net > or use: >      > > E-mail to administrators: CHEMISTRY-REQUEST!^!ccl.net > or use >      >      >      > > > From owner-chemistry@ccl.net Wed Apr 3 10:26:00 2013 From: "Asmund Rohr a.k.rohr+*+ibv.uio.no" To: CCL Subject: CCL: QM/MM calculation setup - solvate or not? - MD or not? Message-Id: <-48517-130403085902-12033-fyMT4w71U7xq7a1V+GVFbA]|[server.ccl.net> X-Original-From: "Asmund Rohr" Date: Wed, 3 Apr 2013 08:59:00 -0400 Sent to CCL by: "Asmund Rohr" [a.k.rohr*o*ibv.uio.no] Dear all, I have a few questions regarding QM/MM calculation setups in general. 1. First, should I solvate the protein with TIP3 waters? Is this really important or could it be enough to include water molecules from the crystal structure? 2. Is it important to neutralize the solvated protein by adding e.g. Na+ or Cl- ? 3. In some calculations MD snapshots are used as starting points for QM/MM calculations. If the crystal structure quality is high - is the MD procedure necessary? If you can suggest any relevant references on the topic, please send me an email. Best regards, Asmund Rohr Department of Biosciences University of Oslo From owner-chemistry@ccl.net Wed Apr 3 13:14:01 2013 From: "Ian Hovell hovell#,#eq.ufrj.br" To: CCL Subject: CCL:G: Using carbon dioxide as an alternative solvent in Gaussian Message-Id: <-48518-130403125836-16606-TL7fmqAOlz/iGNJ0A+nVDw]_[server.ccl.net> X-Original-From: "Ian Hovell" Date: Wed, 3 Apr 2013 12:58:34 -0400 Sent to CCL by: "Ian Hovell" [hovell-#-eq.ufrj.br] Dear Readers, I am investigating the effects of carbon dioxide on small simple hydrocarbon molecules such as methane and ethane. There is a limited list of solvents in Gaussian which can be used and that their static and dynamic dielectric constants can be over ridden when using the SCRF keyword. My question is would replacing these dielectric constants for values corresponding to those for carbon dioxide accurately represent carbon dioxide or are there other considerations I need to take into account? The dielectric constant varies with pressure and temperature does this mean that I would also be able to see the effect of solvent pressure and temperature? Ian Hovell School of Chemistry UFRJ