From owner-chemistry@ccl.net Sun Aug 26 02:16:00 2012 From: "Gregorio =?iso-8859-1?Q?Garc=EDa_Moreno?= gjgarcia%x%ujaen.es" To: CCL Subject: CCL:G: Graphed by Gaussian Message-Id: <-47467-120826021337-14225-5bfWgs+2+qaXZkfLGqB96A%%server.ccl.net> X-Original-From: Gregorio =?iso-8859-1?Q?Garc=EDa_Moreno?= Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sun, 26 Aug 2012 08:13:30 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Gregorio =?iso-8859-1?Q?Garc=EDa_Moreno?= [gjgarcia===ujaen.es] You are wrong! Gaussian is for computational chemistry, not to do graphs. Why do you want this plot with gaussian? It is easier with programs such as excell, origin, sigmaplot, gnuplot. etc.... Or.... do you want to study the reaction with Gaussian from a theoretical perspective?? > > Sent to CCL by: "Nguyen Minh Ly" [nguyenminhly2209]![yahoo.com] > Dear sir, > I'm Ly, Viet Nam > I have made a few chemical experiments. So I have a few parameters which > need > represented by a graph. > For example: I made a chemical reaction between Mg and HCl solution. I > read the > volume of H2 gas which produced every 15 seconds. I need to draw a graph > to > represent the change in volume of H2 gas. I can still do this with Excel. > But I > want to draw the graph with Gaussian 03. > Can you tell me how to do this by Gaussian ? > > Thanks for your helping. From owner-chemistry@ccl.net Sun Aug 26 15:24:01 2012 From: "Guiyu Zhao guiyu.zhao(0)astrazeneca.com" To: CCL Subject: CCL: prediction of peptide structures and protein-protein docking Message-Id: <-47468-120826043056-19228-2XncskCUWmvu6AAUGhs0Jg]![server.ccl.net> X-Original-From: "Guiyu Zhao" Date: Sun, 26 Aug 2012 04:30:54 -0400 Sent to CCL by: "Guiyu Zhao" [guiyu.zhao{:}astrazeneca.com] Dear CCL colleagues, I'm trying to fulfill a request from my colleagues about a 17-membered peptide. They want to get a rough idea about the peptide's 3D structure and, if possible, the binding pose with a cell receptor. I feel the task is chellenging for me not only because I'm a modeler on small molecules and not familiar with protein modeling, but also because we are lack of commercial tools to do peptide structure prediction and protein-protein docking. So first of all, is there any free tool to do such calculations? RosettaDcok and BioLuminate from Schrodinger Inc. are not available to me. Then, is it reallistic to model a peptide's 3D structure without knowing anything about its secondary structure (my colleagues only provided me its sequence)? Thank you in advance for any response. Kind regards, Guiyu Zhao From owner-chemistry@ccl.net Sun Aug 26 15:59:00 2012 From: "John McKelvey jmmckel::gmail.com" To: CCL Subject: CCL:G: MOPAC/MOZYME PBC calculations Message-Id: <-47469-120826121255-20471-xgckZ2hr9Lhtwmlv9HKTMg[]server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 26 Aug 2012 12:12:48 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel]-[gmail.com] Have you tried the latest version of Gaussian for all this as I think it also contains one of the latest MOPAC versions? In MOPAC itself you can use the DENOUT keyword to keep a satisfactory current density and then OLDENS to read YOUR_FILENAME.DEN in to start a subsequent job. You can carve out an input geometry from an archive file (YOUR_FILENAME.ARC). To the best of my knowledge MOPAC does not output intermediate geometries, and I am not aware that it outputs a Hessian that can be read back in. Again, Gaussian included version of MOPAC can likely do all you want. John McKelvey On Fri, Aug 24, 2012 at 6:27 PM, Andrew Yeung andrew.yeung=-=chem.tamu.edu wrote: > > Sent to CCL by: Andrew Yeung [andrew.yeung^^chem.tamu.edu] > Hi all > > I am doing a few PBC calculations on MOPAC, and I was hoping for some > advise. > > Since the system is rather large (and I suppose the initial guess is poor), > I cannot get SCF convergence unless I use the MOZYME keyword. The online > manual (http://openmopac.net/manual/mozyme.html) gives some tips on > multi-step jobs (MOZYME for geometry optimization, then MOPAC, then perhaps > FORCE). > > Since my jobs have started already (MOZYME then FORCE), I want to let it > run, and do the MOPAC equivalent of "geom=allcheck guess=read opt(readfc)" > on the resultant output file(s). Is this possible? How else can I start a > new calculation based on an old one? Should I edit the archive (.arc) file > into a new MOPAC input file? > > Thanks for your comments. > > -- > Andrew Yeung > Donald J. Darensbourg Research Group > Department of Chemistry, Texas A&M University > 3255 TAMU > College Station, TX 77843-3255 > > Tel: 979 845 4837 > Fax: 979 845 0158http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel a gmail.com From owner-chemistry@ccl.net Sun Aug 26 16:49:00 2012 From: "Saman Alavi saman.alavi,+,nrc.ca" To: CCL Subject: CCL:G: NMR calculations with all electron relativistic basis sets for Xe Message-Id: <-47470-120826164320-21834-0umWMV8o7aUCxFfDLEuBbQ(~)server.ccl.net> X-Original-From: "Saman Alavi" Date: Sun, 26 Aug 2012 16:43:18 -0400 Sent to CCL by: "Saman Alavi" [saman.alavi a nrc.ca] Hello CCLers, I've been trying to perform Xe NMR chemical shielding calculations with the triple zeta all-electron basis sets of Partridge and Faegri (NASA Technical Memorandum 103918, 1992)with Gaussian 03. I believe I have the route line and format of the basis set written correctly in the input file. For example, for the reference calculation of Xe in the gas phase, I use: ------------ #p b3lyp/gen NMR Xe reference 0 1 Xe 0.000 0.000 0.000 Xe 0 S 26 1.00 174332000.0000 0.000001 26391340.0000000 0.000004 6068091.0000000 0.000021 1734662.0000000 0.000088 From owner-chemistry@ccl.net Sun Aug 26 17:23:01 2012 From: "Marc Baaden baaden . smplinux.de" To: CCL Subject: CCL: prediction of peptide structures and protein-protein docking Message-Id: <-47471-120826165812-419-idjr5HF6EhHiYKDiQm8/BQ|server.ccl.net> X-Original-From: Marc Baaden Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Sun, 26 Aug 2012 22:59:42 +0200 Mime-Version: 1.0 Sent to CCL by: Marc Baaden [baaden,,smplinux.de] Dear Guiyu Zhao, You may want to try the Pepfold server: http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD/ The current version should work for peptides up to 36 amino acids. Kind regards, Marc Baaden >>> "Guiyu Zhao guiyu.zhao(0)astrazeneca.com" said: >> >> Sent to CCL by: "Guiyu Zhao" [guiyu.zhao{:}astrazeneca.com] >> Dear CCL colleagues, >> >> I'm trying to fulfill a request from my colleagues about a 17-membered pept ide. They want to get a rough idea about the peptide's 3D structure and, i f possible, the binding pose with a cell receptor. >> >> I feel the task is chellenging for me not only because I'm a modeler on sma ll molecules and not familiar with protein modeling, but also because we a re lack of commercial tools to do peptide structure prediction and protein -protein docking. So first of all, is there any free tool to do such calcu lations? RosettaDcok and BioLuminate from Schrodinger Inc. are not availab le to me. Then, is it reallistic to model a peptide's 3D structure without knowing anything about its secondary structure (my colleagues only provid ed me its sequence)? >> >> Thank you in advance for any response. >> >> Kind regards, >> Guiyu Zhao>> >> Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden---smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217