From owner-chemistry@ccl.net Fri Jan 27 00:33:00 2006 From: "Brian Salter-Duke b_duke|-|octa4.net.au" To: CCL Subject: CCL:G: composite energy method with transition metal Message-Id: <-30651-060126220041-12652-rcnfnP8Q9IyCn7cjmJ7ZKA||server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 27 Jan 2006 12:11:27 +1100 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke(!)octa4.net.au] On Thu, Jan 26, 2006 at 07:01:15PM -0500, Young Leh youngleh-#-gmail.com wrote: > Sent to CCL by: "Young Leh" [youngleh]_[gmail.com] > Dear Ccler, > > I have been collecting information on the application of composite energy > methods to transition metals for a long time. All the popular composite > energy methods, Gaussian-n, Complete Basis Set, and multi-coefficent, are > only calibarited with first, second, and third row elements excluding > transition metals. Is there any composite energy method that can be > applied to transition metal at all? Or if I am going to use those methods > to transition metals, how wrong could I be? There are a number of issues here:- 1) Is there a set of molecules with good experimental data to use as a test set? 2) Do the appropriate basis sets exist? There is a proper 6-31G basis now but I'm not sure what to use for 6-311G? 3) Do you mean first transition row only? That might be possible. If you want 2rd and 3rd transition rows I would look to a pseudo-potential composite method. I thought about that once but did not follow through. Brian. > thank you all for the reponse and any suggestion is greatly appreciated. > > Sincerely, > > Young Leh> > > -- Brian Salter-Duke (Brian Duke) b_duke=-=octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. From owner-chemistry@ccl.net Fri Jan 27 01:08:00 2006 From: "karlo Mendoza Falla karlo_999|-|yahoo.es" To: CCL Subject: CCL:G: UV calculations with Gaussian Message-Id: <-30652-060126223204-7070-FEyjc+/TggjDV3qDFEtT0Q()server.ccl.net> X-Original-From: karlo Mendoza Falla Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 27 Jan 2006 03:31:57 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: karlo Mendoza Falla [karlo_999_+_yahoo.es] its possible modify %Mem=x x as equal to any amount in unities GB or MB. is an possibility. your place in the first section : %chk=work1 %Mem=600MB for example... I hope help you , my best wishes for you. Karlo Edward Mendoza Falla. Universidad Nacional mayor de San Marcos. Lima-Peru. Quimica. --- "Anastasios Papadopoulos anastp,,chem.auth.gr" escribió: > Sent to CCL by: Anastasios Papadopoulos > [anastp,+,chem.auth.gr] > Dear CCL users, > > I am running UV calculations of Ag,Cu clusters in > Gaussian 03,using > BP86/lanl2dz method. All calculations abnormally end > during link l914 without > any error message. > Could anybody inform me about the causes of this > problem? > > Yours, > Tasos G. Papadopoulos > > > > -= 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 > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST+*+ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com From owner-chemistry@ccl.net Fri Jan 27 05:34:01 2006 From: "Michel Petitjean ptitjean[-]itodys.jussieu.fr" To: CCL Subject: CCL: Re(2): calculating area of a ring Message-Id: <-30653-060127053042-1480-5MUfiH69YKE+0hQ91eyKPQ(~)server.ccl.net> X-Original-From: Michel Petitjean Date: Fri, 27 Jan 2006 11:30:17 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean]^[itodys.jussieu.fr] To: Subject: CCL: Re(2): calculating area of a ring Nancy Mills asked for a program calculating the area of a flat ring. Matthias Rarey [rarey]^[zbh.uni-hamburg.de] replied: > Assuming your polygon has n points (x[i],y[i]), 0 <=3D i < n, then the > following loop should do the job: > area= 0; > for(i=0; i return (area/2); > > The function works even for a concave polygon, it should be simple,=20 > however (meaning it has no crossing edges). David J Anick [david.anick[A]rcn.com] replied: > Here is a very easy formula for the area of a polygon > based on Green's theorem. > > If the coordinates of the vertices are (in order) > (a1,b1), (a2,b2), (a3,b3), ... , (aN,bN), then back to (a1,b1), > the formula is: > > Area = [(b2-b1)*(a1+a2) + (b3-b2)*(a2+a3) + ... + (b1-bN)*(aN+a1)] / 2 . > > I.e., for each edge of the polygon, you compute (the difference of the > y-coords > times the sum of the x-coords); add these up and divide by 2. It really > works. > Make sure you don't accidentally do (bN-b1) instead for the last step. > You have to list the vertices so that they trace the polygon in a > counterclockwise fashion; if clockwise you get minus the area (or just > ignore orientation but be sure to take the abs value of the answer). Do you assume convexity ? - If yes, either you know the ordered list of extremal points (i.e. the 2D convex hull of the set), or you need to genereate it with a convex hull algorithm. In 2D, you may on the web find many freewares doing that. In 3D, please download RADI from my web site. - If no, you should have a coherent description of the concavities. If you have just a set of points and you need to generate concavities automatically, it is an open problem. In 3D, ALVIS (from Edelsbrunner) provides an excellent solution under the assumption that you are able to fix the arbitrary value of a parameter (a probe sphere radius). If this parameter is null, or too small, you are left to your set of points. If it is infinite, or too big, you retrieve a 3D Delaunay triangulation. Other methods I know have more parameters, and alas the final results depend crucially of these parameters, to be set by the user or by the programmer, because they are not computable from the data only. The non parametric detection of cavities from a set of points if one of the most challenging mathematical problems raised in molecular modeling. At the difference of other math problems, the difficulty is not to solve some set of equations, but rather to exhibit a definition of the cavities in this context. If somebody knows a solution, even in 2D, I would like to hear about it. Thanks. Michel Petitjean, Email: petitjean*|*itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean*|*ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI From owner-chemistry@ccl.net Fri Jan 27 08:25:00 2006 From: "Roman D. Gorbunov gorbunov_._theochem.uni-frankfurt.de" To: CCL Subject: CCL: Scaling factor for normal mode frequency. Message-Id: <-30654-060127082330-1595-qb1yJAWj7Rhgb94hGf3L3w-*-server.ccl.net> X-Original-From: "Roman D. Gorbunov" Sent to CCL by: "Roman D. Gorbunov" [gorbunov(0)theochem.uni-frankfurt.de] Dear All, Does anybody know where/whether one can find the scaling factor for the vibrational frequencies calculated on B3LYP/6-31+G(d) level of theory. The most closest reference that I found is: J. Phys. Chem., Vol. 100, No. 41, 1996. There one can find the scaling factors for HF/6-31+G(d) as well as for B3LYP/6-31G(d), It is close to what I need but not exactly the same. Thank you in advance, Roman. From owner-chemistry@ccl.net Fri Jan 27 11:48:00 2006 From: "Nuno A.G. Bandeira nuno.bandeira]=[ist.utl.pt" To: CCL Subject: CCL: winGAMESS Message-Id: <-30655-060127114653-1548-7dTr0ypoI29Ksm/XxS3uXg_-_server.ccl.net> X-Original-From: "Nuno A.G. Bandeira" Sent to CCL by: "Nuno A.G. Bandeira" [nuno.bandeira_._ist.utl.pt] The new winGAMESS development version R5 (Nov. last year) is now online with accompanying utilities, test files and manuals. Embedded programs like Tinker and VB2000 are in it. You may download it from the GAMESS site as usual. I've been getting emails from several people regarding a few points and I think I should restate this: 1- winGAMESS is a complete port of the current GAMESS release (R5) for Windows. IT IS NOT PC-GAMESS! Do not mistake both. They are entirely different and unrelated in terms of user interface and operability. The official GAMESS website is I think entirely clear on this point and I advise potential users to know this in advance. Do not try to run the binary gamess.06.exe from the command line as you do with pcgamess, it will not work. A DOS batch script needs to be generated first by use of batmaker. Let the *.bat script worry about commands, all you have to do is click (use the mouse, wrist and finger, it's that simple) As I say again this is not pcgamess... read the readme.rtf file before you do anything. 2- Cygwin libraries are, as far as I've read, unable to handle SysV calls in clusters or parallel processing. As such parallel use of winGAMESS with the new ddi libraries is disabled. The old ddi code is however usable for parallel Windows boxes (prof. Ernst Schumacher can tell you more about this). But a special compilation for this is required (email me if you can't do it by yourself). 3- The binaries were compiled for SSE instruction set processors (-msse, -mfpmath=sse) so they should work with the most recent processors from intel/amd. They have been tried and tested on my laptop pentium M and in a P4 with hyperthreading. Special thanks to Grigoriy Zhurko for his continuing help. Check out his program Chemcraft at www.chemcraftprog.com for visualization of gamess outputs. Hope you enjoy it. Regards, -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student * IST,Lisbon From owner-chemistry@ccl.net Fri Jan 27 12:22:00 2006 From: "Axel Mathieu AMathieu|a|tranzyme.com" To: CCL Subject: CCL: HEME group and FAD (Flavine Adenine Dinucleotide) CVFF parameters Message-Id: <-30656-060127094424-3350-zuFBt9uH3taLXj6n3FserA- -server.ccl.net> X-Original-From: "Axel Mathieu" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 27 Jan 2006 08:58:40 -0500 MIME-Version: 1.0 Sent to CCL by: "Axel Mathieu" [AMathieu ~~ tranzyme.com] Hello Cesar, I modeled Cyp's during my graduate studies using InsightII. There was a clear and specific methodology for Heme modeling somewhere in the InsightII manuals (look in the FAQ's if you have access to the electronic versions); I've never modeled FAD but maybe it is there somewhere also. The problem with CVFF for Heme, at least when I was working with it (ca 7 years ago), was the lack of parameters for Fe. The trick if I remember correctly, was to use Ca instead and modify charge distribution on the N's surrounding it. I'll get back to you if I can find the methodology in my old notes. APM -----Original Message----- > From: owner-chemistry---ccl.net [mailto:owner-chemistry---ccl.net] Sent: 26 janvier, 2006 23:14 To: Axel Mathieu Subject: CCL: HEME group and FAD (Flavine Adenine Dinucleotide) CVFF parameters Sent to CCL by: "Cesar Millan" [pachequin{=}gmail.com] Hi every body I'm trying to use InsightII for making some calculations using HEME group and FAD molecules but I don't have any .car files or parameters for those molecules. Does anybody have these files or any hint to construct those molecules on insightII? Thank You everybody.http://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 Fri Jan 27 12:58:01 2006 From: "Chaitanya Krishna A icymist82!=!yahoo.com" To: CCL Subject: CCL: Monte Carlo Codes or Software Message-Id: <-30657-060127093854-2714-meC3g8npnRouv/3MAnwigw:+:server.ccl.net> X-Original-From: Chaitanya Krishna A Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 27 Jan 2006 05:38:49 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Chaitanya Krishna A [icymist82 ~ yahoo.com] Hi all, I would like to know if there are any packages, codes or software that do Monte Carlo simulations preferably which come with the source. After some googling I came across BOSS. Acutally I know of a Monte Carlo suite with a bird as their logo. Now I forgot which. If any one of you knows about it, kindly let me know. Regards, Chaitanya. Indian Institute of Science Bangalore. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Fri Jan 27 13:33:00 2006 From: "Dillen Jan jlmd(0)sun.ac.za JLMD(0)sun.ac.za" To: CCL Subject: CCL: Scaling factor for normal mode frequency. Message-Id: <-30658-060127101129-9213-jfV6tO3fFToEnzxvQTowRw|a|server.ccl.net> X-Original-From: "Dillen Jan " Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Fri, 27 Jan 2006 16:33:00 +0200 MIME-Version: 1.0 Sent to CCL by: "Dillen Jan [jlmd[#]sun.ac.za]" See http://srdata.nist.gov/cccbdb/ Click on Item XIII - Vibrations in the left column. They mention B3LYP/6-31+G** - not exactly what you want but very close. jd > Does anybody know where/whether one can find the scaling > factor for the vibrational frequencies calculated on > B3LYP/6-31+G(d) level of theory. From owner-chemistry@ccl.net Fri Jan 27 14:07:00 2006 From: "Abrash, Samuel sabrash|*|richmond.edu" To: CCL Subject: CCL: Scaling factor for normal mode frequency. Message-Id: <-30659-060127115643-1235-I64NqPhPqtICSUuX0718pQ*server.ccl.net> X-Original-From: "Abrash, Samuel" Date: Fri, 27 Jan 2006 09:54:41 -0500 Sent to CCL by: "Abrash, Samuel" [sabrash~!~richmond.edu] Hi Roman, The NIST Computational Chemistry Comparison and Benchmark Database includes a large list of scaling factors. Click on this link: http://srdata.nist.gov/cccbdb/ to get to the database and then click on vibrations. Best, Sam Abrash -----Original Message----- From: Roman D. Gorbunov gorbunov_._theochem.uni-frankfurt.de Sent: Fri 1/27/2006 8:32 AM To: Abrash, Samuel Cc: Subject: CCL: Scaling factor for normal mode frequency. Sent to CCL by: "Roman D. Gorbunov" [gorbunov(0)theochem.uni-frankfurt.de] Dear All, Does anybody know where/whether one can find the scaling factor for the vibrational frequencies calculated on B3LYP/6-31+G(d) level of theory. The most closest reference that I found is: J. Phys. Chem., Vol. 100, No. 41, 1996. There one can find the scaling factors for HF/6-31+G(d) as well as for B3LYP/6-31G(d), It is close to what I need but not exactly the same. Thank you in advance, Roman. From owner-chemistry@ccl.net Fri Jan 27 14:43:01 2006 From: "Shobe, David dshobe- -sud-chemieinc.com" To: CCL Subject: CCL:G: composite energy method with transition metal Message-Id: <-30660-060127131357-27700-T6e7N3FE/I0xmQSJ/bwuvg]=[server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 27 Jan 2006 19:13:45 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe/./sud-chemieinc.com] 4) As if these weren't enough, there is one more serious problem: the bonding in transition metal species is in general more complex than the bonding in main-group species. With the latter, you can find a Hartree-Fock wave function which, despite its inadequacies, is at least a good place to start from when calculating the correlated wave function. With transition metal species, there is often no H-F wave function which is a suitable starting poitn. It has been proposed to start such calculationswith a multi-determinant wave function (e.g. CASSCF) but AFAIK no one has worked out the details necessary to make this idea into a workable model chemistry. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry=ccl.net [mailto:owner-chemistry=ccl.net] Sent: Friday, January 27, 2006 12:52 AM To: Shobe, David Subject: CCL:G: composite energy method with transition metal Sent to CCL by: Brian Salter-Duke [b_duke(!)octa4.net.au] On Thu, Jan 26, 2006 at 07:01:15PM -0500, Young Leh youngleh-#-gmail.com wrote: > Sent to CCL by: "Young Leh" [youngleh]_[gmail.com] Dear Ccler, > > I have been collecting information on the application of composite > energy methods to transition metals for a long time. All the popular > composite energy methods, Gaussian-n, Complete Basis Set, and > multi-coefficent, are only calibarited with first, second, and third > row elements excluding transition metals. Is there any composite > energy method that can be applied to transition metal at all? Or if I > am going to use those methods to transition metals, how wrong could I be? There are a number of issues here:- 1) Is there a set of molecules with good experimental data to use as a test set? 2) Do the appropriate basis sets exist? There is a proper 6-31G basis now but I'm not sure what to use for 6-311G? 3) Do you mean first transition row only? That might be possible. If you want 2rd and 3rd transition rows I would look to a pseudo-potential composite method. I thought about that once but did not follow through. Brian. > thank you all for the reponse and any suggestion is greatly appreciated. > > Sincerely, > > Young Leh> > > -- Brian Salter-Duke (Brian Duke) b_duke#,#octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Fri Jan 27 15:17:00 2006 From: "Joslyn Y Kravitz jyudenfr++umich.edu" To: CCL Subject: CCL: HEME group and FAD (Flavine Adenine Dinucleotide) CVFF parameters Message-Id: <-30661-060127135928-27056-7s2glx0U4MVwqZfrWI7/Aw_._server.ccl.net> X-Original-From: Joslyn Y Kravitz Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 27 Jan 2006 13:21:34 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Joslyn Y Kravitz [jyudenfr[]umich.edu] The esff force field has parameters for most metals and I am fairly sure that Fe is one of them. The problem is that you can't set the protonation states properly using esff. The way to get around this is to unbond the metal from the rest of the structure and set the protonation states and partial charges for the organic parts using cvff. Then you add the metal back in and correct the charges and protonation states for the atoms to which it is bound by hand and set the potentials and atom types for everything else using esff but retaining the protonation from cvff. You have to use the Discover 3 module rather than the Discover module to do this. I can send a more exact procedure later on if needed. Joslyn Kravitz On Fri, 27 Jan 2006, Axel Mathieu AMathieu|a|tranzyme.com wrote: > Sent to CCL by: "Axel Mathieu" [AMathieu ~~ tranzyme.com] > > Hello Cesar, > > I modeled Cyp's during my graduate studies using InsightII. There was a > clear and specific methodology for Heme modeling somewhere in the > InsightII manuals (look in the FAQ's if you have access to the > electronic versions); I've never modeled FAD but maybe it is there > somewhere also. The problem with CVFF for Heme, at least when I was > working with it (ca 7 years ago), was the lack of parameters for Fe. The > trick if I remember correctly, was to use Ca instead and modify charge > distribution on the N's surrounding it. I'll get back to you if I can > find the methodology in my old notes. > > APM > > -----Original Message----- >> From: owner-chemistry*o*ccl.net [mailto:owner-chemistry*o*ccl.net] > Sent: 26 janvier, 2006 23:14 > To: Axel Mathieu > Subject: CCL: HEME group and FAD (Flavine Adenine Dinucleotide) CVFF > parameters > > Sent to CCL by: "Cesar Millan" [pachequin{=}gmail.com] > Hi every body I'm trying to use InsightII for making some calculations > using HEME group and FAD molecules but I don't have any .car files or > parameters for those molecules. Does anybody have these files or any > hint to construct those molecules on insightII? > > Thank You everybody.http://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 Fri Jan 27 15:52:01 2006 From: "Mohamad Hadi Kassaee mkassaee . gmail.com" To: CCL Subject: CCL: Scaling factor for normal mode frequency. Message-Id: <-30662-060127134856-20741-kHFpkl7C2Iv+RIxPaBmfiw]![server.ccl.net> X-Original-From: Mohamad Hadi Kassaee Content-Type: multipart/alternative; boundary="----=_Part_6639_10198524.1138383804076" Date: Fri, 27 Jan 2006 12:43:24 -0500 MIME-Version: 1.0 Sent to CCL by: Mohamad Hadi Kassaee [mkassaee|*|gmail.com] ------=_Part_6639_10198524.1138383804076 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Roman, NIST (National Institute of Standards and Technology) website has compiled = a big list of scale factors for vibrational frequencies in its Computational Chemistry Comparison and Benchmark Database. It is a free access database and has a lot of combinations between quantum mechanics methods and basis sets for large sets of molecules. This database address: http://srdata.nist.gov/cccbdb/ The list of NIST online databases: http://srdata.nist.gov/gateway/gateway?dblist=3D0 Regards, Mohamad Kassaee Chemical Engineering Department, University of Tennessee at Knoxville Knoxville, TN, USA On 1/27/06, Roman D. Gorbunov gorbunov_._theochem.uni-frankfurt.de < owner-chemistry*ccl.net> wrote: > > Sent to CCL by: "Roman D. Gorbunov" [gorbunov(0)theochem.uni-frankfurt.de= ] > Dear All, > > Does anybody know where/whether one can find the scaling factor for the > vibrational frequencies calculated on B3LYP/6-31+G(d) level of theory. Th= e > most closest reference that I found is: J. Phys. Chem., Vol. 100, No. 41, > 1996. There one can find the scaling factors for HF/6-31+G(d) as well as = for > B3LYP/6-31G(d), It is close to what I need but not exactly the same. > > Thank you in advance, > Roman. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > ------=_Part_6639_10198524.1138383804076 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Dear Roman,
 
NIST (National Institute of Standards and Technology) websit= e has compiled a big list of scale factors for vibrational frequencies in i= ts Computational Chemistry Comparison and Benchmark Database<= /font>. It is a free access database and has a lot of combina= tions between quantum mechanics methods and basis sets for large sets of mo= lecules.
 
This database address: http= ://srdata.nist.gov/cccbdb/
 
The list of NIST online databases: http://srdata.nist.gov/gateway/gateway?dblist=3D= 0
 
Regards,
 
Mohamad Kassaee
Chemical Engineering Department,
University of Tennessee at Knoxville
Knoxville, TN, USA
 

 
On 1/27/06, = Roman D. Gorbunov gorbunov_._theochem.uni-f= rankfurt.de <owner-ch= emistry*ccl.net > wrote:
Sent to CCL by: "Roman D. G= orbunov" [gorbunov(0)theochem.uni-fran= kfurt.de ]
Dear All,

Does anybody know where/whether one can find the = scaling factor for the vibrational frequencies calculated on B3LYP/6-31+G(d= ) level of theory. The most closest reference that I found is: J. Phys. Che= m., Vol. 100, No. 41, 1996. There one can find the scaling factors for HF/6= -31+G(d) as well as for B3LYP/6-31G(d), It is close to what I need but not = exactly the same.

Thank you in advance,
Roman.



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------=_Part_6639_10198524.1138383804076-- From owner-chemistry@ccl.net Fri Jan 27 16:27:01 2006 From: "Sekr. Prof. Joachim Sauer sek.qc*chemie.hu-berlin.de" To: CCL Subject: CCL: Announcement: Symposium on Theoretical Chemistry "Quantum Chemistry - Methods and Applications" Message-Id: <-30663-060127133137-11748-JbmysGzLgSMkXNqIi9yUSQ * server.ccl.net> X-Original-From: "Sekr. Prof. Joachim Sauer" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Fri, 27 Jan 2006 14:52:14 +0100 MIME-Version: 1.0 Sent to CCL by: "Sekr. Prof. Joachim Sauer" [sek.qc~~chemie.hu-berlin.de] 42nd Symposium on Theoretical Chemistry "Quantum Chemistry — Methods and Applications" September 3 – 6, 2006, Erkner (near Berlin) Dear colleague, we announce the 42nd Symposium on Theoretical Chemistry "Quantum Chemistry — Methods and Applications". The Symposium will consist of 12 invited lectures, 22 lectures (20 min) selected from submissions and posters. You are cordially invited to register and submit abstracts for posters / short lectures. Details can be found on the Internet: http://www.chemie.hu-berlin.de/ag_sauer/stc2006/index.html Looking forward to your application, Joachim Sauer (Chairman) -- ------------------------------------------------------------ Silvana Pophal Humboldt-Universitaet zu Berlin Institut fuer Chemie Post: Unter den Linden 6 10099 Berlin Besucher/ Brook-Taylor-Str. 2 Pakete: 12489 Berlin Tel.: +(49) 30-2093-7134 Fax: +(49) 30-2093-7136 e-mail: sek.qc%chemie.hu-berlin.de www.chemie.hu-berlin.de/ag_sauer ------------------------------------------------------------- From owner-chemistry@ccl.net Fri Jan 27 17:02:01 2006 From: "Anthony Fejes fejes|,|zymeworks.com" To: CCL Subject: CCL: Monte Carlo Codes or Software Message-Id: <-30664-060127143211-18459-qcQqvXOXLkucMGqhMnWLkw^^^server.ccl.net> X-Original-From: Anthony Fejes Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 27 Jan 2006 10:42:17 -0800 MIME-Version: 1.0 Sent to CCL by: Anthony Fejes [fejes _ zymeworks.com] The MC suite you're thinking about, with a bird as a logo is probably MCCCS Towhee: http://towhee.sourceforge.net/ Cheers > After some googling I came across BOSS. Acutally I know of a Monte Carlo suite > with a bird as their logo. Now I forgot which. If any one of you knows about > it, kindly let me know. > > Regards, > Chaitanya. -- Anthony Fejes Zymeworks Inc. - A Catalyst in Design 201-1401 West Broadway Ave, Vancouver, B.C. Canada, V6H 1H6 www.zymeworks.com From owner-chemistry@ccl.net Fri Jan 27 17:37:01 2006 From: "Alexander Kollias ackollias,+,gmail.com" To: CCL Subject: CCL: Monte Carlo Codes or Software Message-Id: <-30665-060127151234-6637-Kkku1vjetCuuT0c3Rx3LrQ^^server.ccl.net> X-Original-From: Alexander Kollias Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 27 Jan 2006 14:06:54 -0500 Mime-Version: 1.0 Sent to CCL by: Alexander Kollias [ackollias{=}gmail.com] The following QMC codes are available: QMCMOL: http://www.lct.jussieu.fr/qmcmol/qmcmol/ QMCBEAVER: http://qmcbeaver.sourceforge.net/ CHAMP: http://people.ccmr.cornell.edu/~cyrus/champ.html ZORI:http://www.zori-code.com/ CASINO:http://www.tcm.phy.cam.ac.uk/~mdt26/casino2.html regards, Sasha On Fri, 2006-01-27 at 13:15 -0500, Chaitanya Krishna A icymist82!=! yahoo.com wrote: > Sent to CCL by: Chaitanya Krishna A [icymist82 ~ yahoo.com] > Hi all, > > I would like to know if there are any packages, codes or software that do Monte > Carlo simulations preferably which come with the source. > > After some googling I came across BOSS. Acutally I know of a Monte Carlo suite > with a bird as their logo. Now I forgot which. If any one of you knows about > it, kindly let me know. > > Regards, > Chaitanya. > > Indian Institute of Science > Bangalore. > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com> > > From owner-chemistry@ccl.net Fri Jan 27 18:13:01 2006 From: "STC 2006 stc2006 a chemie.hu-berlin.de" To: CCL Subject: CCL: Announcement: Symposium on Theoretical Chemistry 2006 Message-Id: <-30666-060127115643-61234-8hcO8cvwyhRvjyV1tIubMg]^[server.ccl.net> X-Original-From: STC 2006 Date: Fri, 27 Jan 2006 15:45:35 +0100 Sent to CCL by: STC 2006 [stc2006]~[chemie.hu-berlin.de] 42nd Symposium on Theoretical Chemistry "Quantum Chemistry - Methods and Applications" September 3 - 6, 2006, Erkner (near Berlin) Dear colleague, we announce the 42nd Symposium on Theoretical Chemistry "Quantum Chemistry - Methods and Applications". The Symposium will consist of 12 invited lectures, 22 lectures (20 min) selected from submissions and posters. You are cordially invited to register and submit abstracts for posters / short lectures. Details can be found on the Internet: http://www.chemie.hu-berlin.de/ag_sauer/stc2006/index.html Looking forward to your application, Joachim Sauer (Chairman) ------------------------------------------------------------------------------ Symposium on Theoretical Chemistry "Quantum Chemistry - Methods and Applications" September 3 - 6, 2006, BZ Erkner Symposium Secretariat: Humboldt-Universitaet zu Berlin, Institut fuer Chemie, Unter den Linden 6, D-10099 Berlin, Germany (Visitors/Parcels): Brook-Taylor-Str. 2, 12489 Berlin Tel.: +(49) 30-2093-7134 Fax: +(49) 30-2093-7136 e-mail: stc2006++chemie.hu-berlin.de www: http://www.chemie.hu-berlin.de/ag_sauer/stc2006/ ------------------------------------------------------------------------------ From owner-chemistry@ccl.net Fri Jan 27 22:30:01 2006 From: "Marcel Swart m.swart^^few.vu.nl" To: CCL Subject: CCL: HEME group and FAD (Flavine Adenine Dinucleotide) CVFF parameters Message-Id: <-30667-060127160018-28008-OnhA9A3XFxRffW83JB/8/w-$-server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-9--976062849 Date: Fri, 27 Jan 2006 21:06:50 +0100 Mime-Version: 1.0 (Apple Message framework v553) Sent to CCL by: Marcel Swart [m.swart-.-few.vu.nl] --Apple-Mail-9--976062849 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed Maybe you could try and use the AMBER force field, that does have=20 parameters for both HEME and FAD, or else adapt them from AMBER to InsightII (although=20= I don't know InsightII so don't know how much work/trouble it is). See the standard AMBER page: http://amber.scripps.edu and the contributed parameters website at: http://pharmacy.man.ac.uk/amber The parameter files can be found at the latter page. On Friday, January 27, 2006, at 05:11 AM, Cesar Millan=20 pachequin:-:gmail.com wrote: > Sent to CCL by: "Cesar Millan" [pachequin{=3D}gmail.com] > Hi every body I'm trying to use InsightII for making some calculations=20= > using HEME group and FAD molecules but I don't have any .car files or=20= > parameters for those molecules. Does anybody have these files or any=20= > hint to construct those molecules on insightII? =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Theoretische Chemie (kamer R152) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands T +31-(0)20-5987619 F +31-(0)20-5987629 E m.swart===few.vu.nl W http://www.few.vu.nl/~swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 Starting May 1, 2006: ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-9--976062849 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 Maybe you could try and use the AMBER force field, that does have parameters for both HEME and FAD, or else adapt them from AMBER to InsightII (although I don't know InsightII so don't know how much work/trouble it is). See the standard AMBER page: http://amber.scripps.edu and the contributed parameters website at: http://pharmacy.man.ac.uk/amber The parameter files can be found at the latter page. On Friday, January 27, 2006, at 05:11 AM, Cesar Millan pachequin:-:gmail.com wrote: Sent to CCL by: "Cesar Millan" [pachequin{=3D}gmail.com] Hi every body I'm trying to use InsightII for making some calculations using HEME group and FAD molecules but I don't have any .car files or parameters for those molecules. Does anybody have these files or any hint to construct those molecules on insightII? = Helvetica=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96 Courierdr. Marcel Swart Theoretische Chemie (kamer R152) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands T +31-(0)20-5987619 F +31-(0)20-5987629 E = 1919,1919,FFFFm.swart===few.vu.nl W=20 = 1919,1919,FFFFhttp://www.few.vu.nl/~swart= = Helvetica=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96 = Courier0000,= 4040,8080Starting May 1, 2006: = Courier0000,4040,8080 ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) = Helvetica000= 0,4040,8080=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= --Apple-Mail-9--976062849-- From owner-chemistry@ccl.net Fri Jan 27 23:05:01 2006 From: "Russell D Johnson III russell.johnson===nist.gov" To: CCL Subject: CCL: Scaling factor for normal mode frequency. Message-Id: <-30668-060127164358-20690-YpJe0mX3XftZffj4CekFZg{}server.ccl.net> X-Original-From: Russell D Johnson III Content-Type: text/plain; charset="us-ascii" Date: Fri, 27 Jan 2006 09:52:25 -0500 Mime-Version: 1.0 Sent to CCL by: Russell D Johnson III [russell.johnson_-_nist.gov] Dear Roman, The scaling factors for B3LYP are not sensitive to the basis set (for basis sets 6-31G* and larger). A scaling factor of 0.96 would be appropriate for B3LYP/6-31+G(d). The NIST CCCBDB: http://srdata.nist.gov/cccbdb has scaling factors. The CCCBDB doesn't have values for that basis set, but you can see how little the scaling factors change over several similar basis sets. If you would like a paper reference: KK. Irikura, RD Johnson III, and RN Kacker, J. Phys. Chem. 109(37), 8430-8437, 2005 illustrates the same invariance. At 08:35 2006-01-27, you wrote: >Sent to CCL by: "Roman D. Gorbunov" [gorbunov(0)theochem.uni-frankfurt.de] >Dear All, > >Does anybody know where/whether one can find the scaling factor for the vibrational frequencies calculated on B3LYP/6-31+G(d) level of theory. The most closest reference that I found is: J. Phys. Chem., Vol. 100, No. 41, 1996. There one can find the scaling factors for HF/6-31+G(d) as well as for B3LYP/6-31G(d), It is close to what I need but not exactly the same. Dr. Russell D. Johnson III Research Chemist National Institute of Standards and Technology Computational Chemistry Group 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301+975-2513 fax:301+869-4020 email: russell.johnson/./nist.gov From owner-chemistry@ccl.net Fri Jan 27 23:40:00 2006 From: "=?ISO-8859-1?Q?Romelia_Salom=F3n_Ferrer?= romesalomon|a|gmail.com" To: CCL Subject: CCL: Monte Carlo Codes or Software Message-Id: <-30669-060127181719-15840-AneSJK6lo+Tu27W4mdsDmw[]server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Romelia_Salom=F3n_Ferrer?= Content-Type: multipart/alternative; boundary="----=_Part_3254_4683675.1138400503225" Date: Fri, 27 Jan 2006 14:21:43 -0800 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Romelia_Salom=F3n_Ferrer?= [romesalomon++gmail.com] ------=_Part_3254_4683675.1138400503225 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi what kind of monte carlo calculation are you thinking about?... if it is quantum monte carlo then the code's name is zori and it does have a bird as it logo... here is our website http://zori-code.com, let me know if this is what you're looking for and specially if you'd like to use it... -- **************************************** Romelia Salomon 13 Gilman Hall Pitzer Center , Chemistry Department UC Berkeley Tel: (510)642-5911 On 1/27/06, Chaitanya Krishna A icymist82!=3D!yahoo.com < owner-chemistry{:}ccl.net> wrote: > > Sent to CCL by: Chaitanya Krishna A [icymist82 ~ yahoo.com] > Hi all, > > I would like to know if there are any packages, codes or software that do > Monte > Carlo simulations preferably which come with the source. > > After some googling I came across BOSS. Acutally I know of a Monte Carlo > suite > with a bird as their logo. Now I forgot which. If any one of you knows > about > it, kindly let me know. > > Regards, > Chaitanya. > > Indian Institute of Science > Bangalore. > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > -- **************************************** Romelia Salomon 13 Gilman Hall Pitzer Center , Chemistry Department UC Berkeley Tel: (510)642-5911 ------=_Part_3254_4683675.1138400503225 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi

what kind of monte carlo calculation are you thinking about?... if it is quantum monte carlo then the code's name is zori and it does have a bird as it logo... here is our website htt= p://zori-code.com, let me know if this is what you're looking for and specially if you'd like to use it...

--
****************************************
Romelia Salomon
13 Gilman Hall
Pitzer Center ,
Chemistry Department
UC Berkeley
Tel: (510)642-5911

On 1/27/06, Chaitanya Krishna A icymist82!=3D!yahoo.com &= lt;owner-chemistry{:}ccl.net&g= t; wrote:
Sent to CC= L by: Chaitanya Krishna A [icymist82 ~ yahoo.c= om ]
Hi all,

I would like to know if there are any packages, cod= es or software that do Monte
Carlo simulations preferably which come wit= h the source.

After some googling I came across BOSS. Acutally I kno= w of a Monte Carlo suite
with a bird as their logo. Now I forgot which. If any one of you knows = about
it, kindly let me know.

Regards,
Chaitanya.

India= n Institute of Science
Bangalore.

_______________________________= ___________________
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RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

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--
**********************= ******************
Romelia Salomon
13 Gilman Hall
Pitzer Center ,
Chemistry Depar= tment
UC Berkeley
Tel: (510)642-5911 ------=_Part_3254_4683675.1138400503225--