From owner-chemistry@ccl.net Sat Dec 3 06:00:01 2011 From: "Vera Cathrine vera.cathrine]^[yahoo.com" To: CCL Subject: CCL: G09: PES rigid scan Message-Id: <-45973-111203055851-5597-0d2i9B2IQ+n82GbE9nGxKA[a]server.ccl.net> X-Original-From: "Vera Cathrine" Date: Sat, 3 Dec 2011 05:58:50 -0500 Sent to CCL by: "Vera Cathrine" [vera.cathrine:+:yahoo.com] Dear All, I am having some difficulties for defining the proper scan variable in my z-matrix input file. The problem is in defining some independent variables. Is it possible to do PES rigid scan in G09 using Cartesian coordinates? Doing relaxed PES scan using Cartesian coordinate is easy by taking advantage of modredundant options in opt or geom keywords. Is there any similar way to define the variable in Cartesian coordinate input? Any suggestion is greatly appreciated. happy weekend, Vera From owner-chemistry@ccl.net Sat Dec 3 16:07:01 2011 From: "quartarolo..unical.it" To: CCL Subject: CCL:G: wb97XD in g09 Message-Id: <-45974-111202161356-2578-ttpvJCbchIGac3BQn+J/7g(0)server.ccl.net> X-Original-From: quartarolo{}unical.it Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 02 Dec 2011 22:13:45 +0100 MIME-Version: 1.0 Sent to CCL by: quartarolo^_^unical.it Hi, I'm just doing a single point calculation. The program stops at the beginning.. So also declaring pop=readradii and lutetium VdW radii, it doesn't work. thanks Quartarolo Domenico > Hi, > > I assume you are doing some population computations, so here is what > you need to do: > 1) On the command route, add the readradii flag under pop, e.g > Pop(bla,bla,bla,readradii). > 2) At the end of your input type the atom name and radius, e.g. Lu XX. > 3) Do some research regarding the radius value. I never used Lu on my > calculations. > > That's all, > Best regards, > > On Thu, Dec 1, 2011 at 10:40 AM, quartarolo|a|unical.it > wrote: >> >> Sent to CCL by: quartarolo _ unical.it >> Dear all, >> I'm running a calculation with Gaussian09 for a Lutetium complex using the >> wB97XD functional. >> The program stops with the following message: >> "R6DR0: No vdW radius available for IA= 71". >> Is there a way to define this parameter manually in the input file and >> eventually where to search for vdW radius of lutetium. >> >> best regards >> >> Quartarolo Domenico >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> >> >> >> **** Riservatezza / Confidentiality **** >> In ottemperanza al D.Lgs. n. 196 del 30/6/2003 in materia di protezione dei >> dati personali, le informazioni contenute in questo messaggio sono >> strettamente riservate ed esclusivamente indirizzate al destinatario >> indicato (oppure alla persona responsabile di  rimetterlo al destinatario). >> Vogliate tener presente che qualsiasi uso, riproduzione o divulgazione di >> questo messaggio e' vietato. Nel caso in cui aveste ricevuto questo >> messaggio per errore, vogliate cortesemente avvertire il mittente e >> distruggere il presente  messaggio.>    >       > >> Job: http://www.ccl.net/jobsConferences: >> http://server.ccl.net/chemistry/announcements/conferences/>    > >> > > > > -- > João Henriques, MSc in Biochemistry > Faculty of Science of the University of Lisbon > Department of Chemistry and Biochemistry > C8 Building, Room 8.5.47 > Campo Grande, 1749-016 Lisbon, Portugal > E-mail: joao.henriques.32353#%#gmail.com / jmhenriques#%#fc.ul.pt > http://intheochem.fc.ul.pt/members/joaoh.html> > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. **** Riservatezza / Confidentiality **** In ottemperanza al D.Lgs. n. 196 del 30/6/2003 in materia di protezione dei dati personali, le informazioni contenute in questo messaggio sono strettamente riservate ed esclusivamente indirizzate al destinatario indicato (oppure alla persona responsabile di rimetterlo al destinatario). Vogliate tener presente che qualsiasi uso, riproduzione o divulgazione di questo messaggio e' vietato. Nel caso in cui aveste ricevuto questo messaggio per errore, vogliate cortesemente avvertire il mittente e distruggere il presente messaggio. From owner-chemistry@ccl.net Sat Dec 3 16:41:00 2011 From: "Cory Pye cpye[#]ap.smu.ca" To: CCL Subject: CCL: How to calculate the independent degrees of freedom of a molecule? Message-Id: <-45975-111203163124-29254-TFPeJ0+EdcouhC4YMZkPHg .. server.ccl.net> X-Original-From: Cory Pye Content-Transfer-Encoding: 8bit Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Date: Sat, 3 Dec 2011 17:39:25 -0400 (AST) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye++ap.smu.ca] Jun, I think that the number of parameters must be the same as the number of totally symmetric vibrational modes of the molecule. Unfortunately I don't have a proof for you, but if you take the space spanned by all the totally symmetric vibrations, then it must be the space spanned by the coordinates as well. -Cory On Sat, 3 Dec 2011, Jun Zhang coolrainbow * yahoo.cn wrote: > Hello everyone:   For a nonlinear N-atom molecule there are 3N-6 internal degrees of freedom, of course.  However, for a point group-constraint molecule, such as C2v H2O, there are only 2 independent degrees of freedom. So, is there a systematic way to determine the number and the contents of independent degrees of freedom of an arbitarily symmetry-constraint molecule? I heard that some knowledge like Polya theorem are requied, but I am not sure. It will be better if some reviews can be reccommended.   Thank you in advance. Any suggestions will be appreciated.   Best regards!   ---------------------------------------------------------------- Jun Zhang (coolrainbow^-^yahoo.cn) Computational Chemistry Group No.94, Weijinlu Nankai University Tianjin, China ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye-.-crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Sat Dec 3 19:51:00 2011 From: "lyzhao lyzhao-*-zjnu.cn" To: CCL Subject: CCL: How to calculate the independent degrees of freedom of a molecule? Message-Id: <-45976-111203194952-2098-sg9SvisPBZb/aP3qxoK4lg..server.ccl.net> X-Original-From: lyzhao Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Sun, 4 Dec 2011 08:49:45 +0800 Mime-Version: 1.0 Sent to CCL by: lyzhao [lyzhao]~[zjnu.cn] Dear Dr. Zhang, I am not sure whether you have seen this "http://en.wikipedia.org/wiki/Degrees_of_freedom_(physics_and_chemistry)" Best regards, Youzhao Lan 2011-12-04 08:47:09 Sender: Jun Zhang coolrainbow * yahoo.cn Date: 2011å¹´12月3æ—¥(星期六) 上åˆ9:11 To: Lan, Youzhao Subject: CCL: How to calculate the independent degrees of freedom of a molecule? Hello everyone: For a nonlinear N-atom molecule there are 3N-6 internal degrees of freedom, of course. However, for a point group-constraint molecule, such as C2v H2O, there are only 2 independent degrees of freedom. So, is there a systematic way to determine the number and the contents of independent degrees of freedom of an arbitarily symmetry-constraint molecule? I heard that some knowledge like Polya theorem are requied, but I am not sure. It will be better if some reviews can be reccommended. Thank you in advance. Any suggestions will be appreciated. Best regards! ---------------------------------------------------------------- Jun Zhang (coolrainbow^-^yahoo.cn) Computational Chemistry Group No.94, Weijinlu Nankai University Tianjin, China From owner-chemistry@ccl.net Sat Dec 3 21:16:01 2011 From: "Nancy nancy5villa[-]gmail.com" To: CCL Subject: CCL: Ice Structure Message-Id: <-45977-111203211247-21600-rFdwrv37CCmUMecNbYd9AQ::server.ccl.net> X-Original-From: Nancy Content-Type: multipart/alternative; boundary=0016e652ff0e45330004b33abce4 Date: Sat, 3 Dec 2011 18:12:34 -0800 MIME-Version: 1.0 Sent to CCL by: Nancy [nancy5villa . gmail.com] --0016e652ff0e45330004b33abce4 Content-Type: text/plain; charset=ISO-8859-1 Hi All, I would like to perform molecular docking to an ice crystal surface; does anyone know if such a structure file can be obtained online? Thanks, Nancy --0016e652ff0e45330004b33abce4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi All,

I would like to perform molecular docking to an ice crystal surface;=A0does= anyone know if such a structure file can be obtained online?

Thanks,
=
Nancy

=


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