From chemistry-request@server.ccl.net Fri Mar 30 14:38:33 2001 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2UJcXD16592 for ; Fri, 30 Mar 2001 14:38:33 -0500 Received: from [130.126.120.225] (dhcp-20.ks.uiuc.edu [130.126.120.225]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id f2UJcXV09619 for ; Fri, 30 Mar 2001 13:38:33 -0600 (CST) Mime-Version: 1.0 X-Sender: brunner@mailhost.ks.uiuc.edu (Unverified) Message-Id: Date: Fri, 30 Mar 2001 13:38:33 -0600 To: chemistry@ccl.net From: biocore@ks.uiuc.edu Subject: ANN: BioCoRE now includes remote job submission Content-Type: text/plain; charset="us-ascii" ; format="flowed" Urbana, Illinois - The Theoretical Biophysics Group at the University of Illinois is proud to announce the latest updates to the BioCoRE web-based collaborative research environment. Since the initial release in March of 2000, we have added significant new features, as well as many minor improvements and features suggested by our users. The following features are the most important additions to the BioCoRE environment. + Job submission and monitoring. BioCoRE now allows you to submit NAMD simulation jobs to your computer accounts on the PSC T3E and the NCSA Origin 2000. After submitting jobs through BioCoRE, you may check back to see whether they have run, and view the output of the jobs as they run. Soon we will be adding a graphical viewer applet for NAMD jobs, and support for more computer systems and applications. + A Java-based Control Panel. This control panel starts up when you first log in to BioCoRE, and provides several convenient features. The control panel provides a cross-project view of all your projects, so you can easily find which projects have changed recently. You can also determine at a glance who else is currently logged in to your projects. The control panel also provides a live chat capability, and notifies you with color and an alert sound when new information is added to any of your projects. + Storing (publishing) molecular visualization views (from VMD) to the BioCoRE notebook. Now, when you launch VMD through BioCoRE you will be presented with an additional window that allows you to publish a molecular state to BioCoRE. Later, any member of your project may retrieve that view from the Message Board. In the Message Board you can select `Saved VMD Sessions' from the drop-down box and choose a published state that you wish to view. Currently this feature is only supported on Unix versions of VMD, but this will soon be available on more platforms. We also have many interesting features planned. For additional information, or to obtain a BioCoRE account, please visit the BioCoRE website at . The Theoretical Biophysics group encourages BioCoRE users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to biocore@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From chemistry-request@server.ccl.net Fri Mar 30 18:45:00 2001 Received: from water.cc.mcgill.ca ([132.206.27.29]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2UNj0D17206 for ; Fri, 30 Mar 2001 18:45:00 -0500 Received: from ariya430 (ariya430.Chem.McGill.CA [132.206.175.28]) by water.cc.mcgill.ca (8.11.1/8.11.0) with SMTP id f2UNj0R15649 for ; Fri, 30 Mar 2001 18:45:00 -0500 (EST) Message-Id: <200103302345.f2UNj0R15649@water.cc.mcgill.ca> From: "Alexei Khalizov" Organization: Chemistry Dept., McGill University To: chemistry@ccl.net Date: Fri, 30 Mar 2001 18:48:34 -0500 MIME-Version: 1.0 Content-type: text/enriched; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Summary: Reduced moment of inertia Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01d) Dear all, I received two advices on how to calculate the reduced moment of inertia for free rotation of chemical bond - thanks a lot! They are given in the end of this message. Frankly speaking, I am still confused. In order to calculate the reduced moment of inertia I(r) one needs the moments of inertia of both fragments about SOME axis I(r)=I1*I2/(I1+I2). According to [1] the bond connecting fragments should be used as an axis, while other sources [2,3] recommend to use separate axes for each fragment, each axis parallel to the bond connecting fragments and passing through the center of mass of corresponding fragment. There is no difference between these aproaches for molecules alike ethane, but in general case (e.g. 1,2-dichloroethane) they lead to significantly different results. Moreover, HROTOR utility included in POLYRATE gives a third different value: 1,2-dichloroethane ------------------------------------------------------------ Method I(r), amu A**2 Q(fr) ------------------------------------------------------------ Method [1] 50.86 44.32 Method [2,3] 16.44 25.20 HROTOR 87.34 58.06 ------------------------------------------------------------ Where is truth? Best regards, Alexei [1] 0100,0100,0100MS Sans Serif Gilbert, S. C. S. Theory of unimolecular and recombination reactions; Blackwell scientific publication: 1990. Arial [2] 0100,0100,0100MS Sans Serif Benson, S. W. Thermochemical kinetics, 2nd ed.; Wiley- Interscience: New York, 1976. Arial [3] Herschbach, D.R., Johnston, H.S., Pitzer, K.S., Powell, R.E. Theoretical pre-exponential factors for twelve bimolecular reactions. J. Chem. Phys., 25(4), 736 (1956) ----------------------------------------------- GEOM is intended to be used with UNIMOL and hence calculates the Ir appropriate for its implementation of variational RRKM theory. for other cases, I normally use a spreadsheet and calculate ir = sum m(x^2+ ...) etc directly. for something as simple as H2O2, this is very fast. :-) for more complicated molecules use something like Chem3d (or similar 3-d modelling program) to get the x,y,z coordinates you want. Chem3d even will move the molecule so that a chosen bond is coincident with a specified axis ... and then put the coordinates into a spreadsheet as before. Kieran ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA 0000,8000,0000mailto:lim@deakin.edu.au 0000,8000,0000http://www.deakin.edu.au/~lim ------------------------------------------------------ You can try the routine implemented in POLYRATE (0000,8000,0000http://comp.chem.umn.edu/polyrate/). It is described in the manual of that program (accessible in the same page) and you will find also several references to how it is done. Jordi - Jordi Villa i Freixa 0000,8000,0000jorgevil@usc.edu 0000,8000,0000http://laetro.usc.edu/wgroup/people/jorgevil Department of Chemistry, University of Southern California Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 ------------------------- Dr. Alexei Khalizov Department of Chemistry McGill University, 801 Sherbrooke St. W., Montreal, Quebec, CANADA, H3A 2K6 Phone: (514) 398-6920 Fax: (514) 398-2382 From chemistry-request@server.ccl.net Fri Mar 30 19:25:09 2001 Received: from web13408.mail.yahoo.com ([216.136.175.66]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f2V0P9D17298 for ; Fri, 30 Mar 2001 19:25:09 -0500 Message-ID: <20010331002509.80608.qmail@web13408.mail.yahoo.com> Received: from [128.97.147.223] by web13408.mail.yahoo.com; Fri, 30 Mar 2001 16:25:09 PST Date: Fri, 30 Mar 2001 16:25:09 -0800 (PST) From: eric hu Subject: problem on locating diradical transition state by DFT To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, All I'm working on a di-phenyl substituted cyclobutane diradical intermediate which can either cleavage or cyclize to different products. B3LYP/6-31g* calculation shows that the singlets are more stable than triplets based on the projected species. Now I have trouble finding the transition state leading to the cyclization pathway. The similar trouble has been reported in literature on the similar radical cation or diradical system. After coordinate-driving from product, I chose some points (with biggest force constants) from molden to do the transition state opitimization . However, I still can't get the resonable transition states. I hope there're other ways to deal with this problem. Thanks in advance! Eric __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/?.refer=text From chemistry-request@server.ccl.net Sat Mar 31 00:38:48 2001 Received: from mx1.ustc.edu.cn ([61.132.182.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2V5bnD17869 for ; Sat, 31 Mar 2001 00:37:51 -0500 Received: from BOC4 ([202.38.66.112]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with SMTP id OAA17805 for ; Sat, 31 Mar 2001 14:22:25 -0800 Message-ID: <00e701c0b9a4$a0f8f820$704226ca@boc.ustc.edu.cn> From: "Jim Fan" To: Subject: sum: setup cluster & avoid g98 error l9999 Date: Sat, 31 Mar 2001 13:37:08 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id f2V5cmD17870 Dear CCLers: Some time ago I posted the question about how to setup a cluster and how to avoid the error of gaussian 98 link 9999. Now I have solved the error l9999 problem by opt(calcall). Thanks for ccl and you all. I wrote the following question: ---------- Forwarded message ---------- From: "Fan Jianmiao" To: Sent: Thursday, March 22, 2001 8:16 PM Subject: CCL:setup a cluster and avoid g98 error link 9999 > Dear CCLers: > > I want to get some help on how to establish a cluster and how to avoid > the error of gaussian 98 link 9999. > > Our lab needs a cluster running gaussian to get a better calculating > envirement. But we haven't enough money, we want to buy some PC and form a > small cluster. But now I don't know the price of Gaussian in parallel(can it > sell to china?) and whether there is any other programs needed. Currently we > have buy four PCs(each is equipted with 2 processors of pIII933 and 768M > SDRAM) and a network switcher. But I haven't installed any software for > paralleling yet. I wonder, how shall I make up the system? > > Another problem is how to avoid the error of g98 link 9999. This error > is very common in our work. Usually we change the iop parameter, but it works > not alwaysly. We found if the start geometry is not very good then maybe this > problem will be conquered. And if the start geometry is similler to the finial > , it will not come to a normail termination then. Why? Puzzling problem! > I often saw this infomation on my screen: > " Error termination request processed by link 9999. > Error termination via Lnk1e in /usr/g98/l9999.exe. > Job cpu time: 1 days 1 hours 39 minutes 8.0 seconds. > File lengths (MBytes): RWF= 824 Int= 0 D2E= 0 Chk= 7 Scr= 1" > > What shall I do after I failed changing the iop parameter?If the geometry should > not be wrong, how can I manage to overcome it? > > If there's anyone can give me some suggestion or comments on it, I would > be very appreciated. > > Thanks for all in advance. > With My Best Regards, > > Sincerely yours, > Jim Fan I received the following answers ---------- Forwarded message ---------- Date: Thu, 22 Mar 2001 23:06:43 +0100 From: Bernd Schubert To: Fan Jianmiao Subject: Re: CCL:setup a cluster and avoid g98 error link 9999 Hi, I think for running gaussian parallel on a cluster you need the LINDA program sold by the gaussian people (for pricing have a look at: http://www.gaussian.com/linda.htm) I think your problem with link 9999 depends on the type of job you run. I'm doing a lot of dft calculations and very often the energy of of the geometry optmisations is not converging. On the contrary the force constants and the energy begin to oscillate. Without a maxiumum of geometry optimisations such job could run for a very long time without finding an end. If you are also doing this kind of jobs (dft or hf calculations) then have a look on your output file. At the end of the last geometry should be mentioned that the maximum number of geometry optimisations is exceeded. The maximum number of geom. calculations is controlled by the keyword opt(MaxCyc=N). To make the energy better converging it is very often helpful to calculate the hesse matrix controlled by the keyword opt(calcfc) - only before the first geom. optmisation or by opt(calcall) - before every geom. optimisation - or by iop(1/40=N) - every N steps, also possible when analytical calculations of the hesse matrix are not possible. An other (and additional to the first suggestions) possibility to make gaussian better finding the minimum is to reduce the maximum stepsize between the geometry optimisations controlled by iop(1/8=N) - opt(stepsize=N) is not working. I have made good experience with iop(1/8=10). I hope that this is your problem and that it might help you, Best regards, Bernd ---------- Forwarded message ---------- Date: Thu, 22 Mar 2001 22:28:55 -0800 From: Roy Jensen To: Jianmiao Fan Subject: Re: How to avoid g98 error link 9999 On Fri, 23 Mar 2001 13:05:25 +0800 (CST), you wrote: > Dear Jensen: > Thanks for your help.I have attched the input and output file. > The job is terminated by steps exceeded. How can I get a normal > termination? > > On Thu, 22 Mar 2001, Roy Jensen wrote: > > > Jim > > > > What is the input line for the failed job? Send me that and the > > complete output file and I will see what I can do about your error > > termination problem. > > > > Roy Jensen > > > > With My Best Regards, > > Sincerely yours, > Jim Fan Jim The input geometry appears to be too far from the optimized structure. Gaussian calculates the force constants once and uses them for the remainder of the run. You have two options: 1) Step 19, 22, and 33 came close to converging. Use any of these geometries as the initial geometry and restart the job. 2) Use opt(calcall) to get gaussian to calculate the force constants at ever step. You do not need to do a second freq calculation; it is automatically done with calcall. This method is time consuming but should work for most any input geometry. Best of luck, Roy Jensen ---------- Forwarded message ---------- Date: Wed, 28 Mar 2001 09:42:52 -0500 From: Jerry Lipchus To: Fan Jianmiao Subject: Linda for Gaussian Dear Fan Jianmiao(Jim_Fan) , Linda is available for download at : http://www.sca.com/site/downloads/index.html LINDA License xxxx xxxx xxxx xxxxxx xxxxx xxxxxx x xxxx xxxx Midnight of May 28, 2001, exclusive -- Scientific Computing Associates 265 Church Street New Haven, CT 06511 Technical Support lsupport@sca.com Tel: (203)777-7442 Fax: (203)776-4074 Thank You Best regards, Jerry Lipchus Director of Sales Scientific Computing Associates, Inc. 265 Church Street Suite 1010 New Haven, CT 06510 lipchus@sca.com 203-777-7442 ext 275 ------------------------------------------------ ------------------------------------------------ With My Best Regards, Sincerely yours, Jim Fan ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fan Jianmiao(Jim_Fan) Department of Chemistry East Campus,USTC Hefei,Anhui,230026,P.R.China Tel:86-551-3654322(dorm) E-Mail:jim_fan@263.net 86-551-3606640(lab) Http://boc.ustc.edu.cn/members/jim_fan/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ I am an undergraduate student. From chemistry-request@server.ccl.net Sat Mar 31 09:38:18 2001 Received: from mail.iitk.ac.in ([210.212.54.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2VEcED20778 for ; Sat, 31 Mar 2001 09:38:15 -0500 Received: from qasid.cc.iitk.ac.in (qasid.cc.iitk.ac.in [172.31.1.16]) by mail.iitk.ac.in (8.9.2/8.9.2) with ESMTP id UAA05822 for ; Sat, 31 Mar 2001 20:12:32 +0530 (IST) Received: from CHINMOY ([172.31.76.193]) by qasid.cc.iitk.ac.in (8.9.2/8.9.2) with SMTP id TAA19651 for ; Sat, 31 Mar 2001 19:58:14 +0530 (IST) Message-ID: <001901c0b9ef$c4a565b0$c14c1fac@CHINMOY> From: "chinmoy ranjan" To: Subject: summary of software to view metal centres of proteins Date: Sat, 31 Mar 2001 20:05:00 +0530 Dear CClers, Few days earlier Ihad posted a message. I n responce I got the following info . Thanks for the suggesstions. The following is the list of suggesstions that I recieved: Dear CCLers, I am trying to see the exact architecture of active site of a protein . Could any one tell me any software or tool (preferably free )through which I could view the exact metal centre of the protein. I tried to edit the PDB file and view the metal centre using rasmol but without much success. Thanks in advance. Greetings, The program Ligplot from the Thorton lab prepares a nice schematic drawing in 2D showing the protein environment of a ligand (reading the info from a PDB file). The URL I have (it is olda - may have been changed) is http://www.biochem.ucl.ac.uk/~mcdonald/ Mihaly Mezei, Dept. of Physiology & Biophysics, Mount Sinai School of = Medicine Voice: (212) 241-2186 Fax: (212) 860-3369| WWW: http://adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01 Ranjan, I guess VMD should do the job. I am pretty sure it is a freeware, you may want to check that. Normally, InsightII or Quanta does this effectively, these are not freeware though.. Another possibility is PDB viewer. Lakshmi ... SUBJECTS WHICH DISCLOSE THEIR FULL POWER, MEANING AND BEAUTY AS SOON AS THEY ARE PRESENTED TO THE MIND HAVE VERY LITTLE OF THOSE QUALITIES TO DISCLOSE. -- CHARLES DUTTON (1882) 0 *************************=20 Lakshmi S Devi Kesavan=20 Graduate Student 1012, 27th Ave SE, Department of Chemistry Apt # A 207, Pleasant Street S.E, Minneapolis,=20 University of Minnesota MN-55414=20 Minneapolis, MN 55455-0431 Off # : 612-625-5325=20 Jim Kress: WebLabViewerLite ( http://www.msi.com/life/products/weblab/viewer/register/lite/download_lite.html ) VMD ( http://www.ks.uiuc.edu/Research/vmd/ ) gOpenMol ( http://laaksonen.csc.fi/gopenmol/gopenmol.html ) Jim Dear Chinmoy, You can try WebLab: It is free, run on PC-Windows and you can download it from: www.msi.com Bye Marco CHINMOY RANJAN INDIAN INSTITUTE OF TECHNOLOGY KANPUR From chemistry-request@server.ccl.net Sat Mar 31 12:42:12 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2VHgCD21509 for ; Sat, 31 Mar 2001 12:42:12 -0500 Received: from web9610.mail.yahoo.com (web9610.mail.yahoo.com [216.136.129.189]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with SMTP id MAA10603 for ; Sat, 31 Mar 2001 12:41:55 -0500 (EST) Message-ID: <20010331174150.35348.qmail@web9610.mail.yahoo.com> Received: from [194.177.32.67] by web9610.mail.yahoo.com; Sat, 31 Mar 2001 19:41:50 CEST Date: Sat, 31 Mar 2001 19:41:50 +0200 (CEST) From: =?iso-8859-1?q?djamel=20leroul?= Subject: demande de formulaire de preinscription en npostgraduation To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit MEKLA on the 15.02.2000 Sir:LEROUL Djamel CASE POSTALE N 18 15350 mekla t.o Algeria Fax 026.30.24.45 E-mail:dleroul@ifrance.fr Object:demande of form of preregistration there postgraduation in your ecole for the2001/2002 Academic year. SIR J ; have honor to demande to your honorable personne of to send a request form dmittance inpostgraduat cycle in your etablissement for the 2001/2002 academic year In wait of Your mail; please approve sir; expression of my best regards. ___________________________________________________________ Do You Yahoo!? -- Pour dialoguer en direct avec vos amis, Yahoo! Messenger : http://fr.messenger.yahoo.com From chemistry-request@server.ccl.net Sat Mar 31 12:45:55 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2VHjtD21569 for ; Sat, 31 Mar 2001 12:45:55 -0500 Received: from web9611.mail.yahoo.com (web9611.mail.yahoo.com [216.136.131.10]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with SMTP id MAA10635 for ; Sat, 31 Mar 2001 12:45:43 -0500 (EST) Message-ID: <20010331174539.92266.qmail@web9611.mail.yahoo.com> Received: from [194.177.32.68] by web9611.mail.yahoo.com; Sat, 31 Mar 2001 19:45:39 CEST Date: Sat, 31 Mar 2001 19:45:39 +0200 (CEST) From: =?iso-8859-1?q?djamel=20leroul?= Subject: demande de formulaire de preinscription en npostgraduation To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit MEKLA on the 15.02.2000 Sir:LEROUL Djamel CASE POSTALE N 18 15350 mekla t.o Algeria Fax 026.30.24.45 E-mail:dleroul@ifrance.fr Object:demande of form of preregistration there postgraduation in your ecole for the2001/2002 Academic year. SIR J ; have honor to demande to your honorable personne of to send a request form dmittance inpostgraduat cycle in your etablissement for the 2001/2002 academic year In wait of Your mail; please approve sir; expression of my best regards. ___________________________________________________________ Do You Yahoo!? -- Pour dialoguer en direct avec vos amis, Yahoo! Messenger : http://fr.messenger.yahoo.com From chemistry-request@server.ccl.net Sat Mar 31 12:51:14 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2VHpED21616 for ; Sat, 31 Mar 2001 12:51:14 -0500 Received: from web9604.mail.yahoo.com (web9604.mail.yahoo.com [216.136.129.183]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with SMTP id MAA10666 for ; Sat, 31 Mar 2001 12:50:57 -0500 (EST) Message-ID: <20010331175052.69236.qmail@web9604.mail.yahoo.com> Received: from [194.177.32.67] by web9604.mail.yahoo.com; Sat, 31 Mar 2001 19:50:52 CEST Date: Sat, 31 Mar 2001 19:50:52 +0200 (CEST) From: =?iso-8859-1?q?djamel=20leroul?= Subject: demande de formulaire de preinscription en npostgraduation To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit MEKLA on the 15.02.2000 Sir:LEROUL Djamel CASE POSTALE N 18 15350 mekla t.o Algeria Fax 026.30.24.45 E-mail:dleroul@ifrance.fr Object:demande of form of preregistration there postgraduation in your ecole for the2001/2002 Academic year. SIR J ; have honor to demande to your honorable personne of to send a request form dmittance inpostgraduat cycle in your etablissement for the 2001/2002 academic year In wait of Your mail; please approve sir; expression of my best regards. ___________________________________________________________ Do You Yahoo!? -- Pour dialoguer en direct avec vos amis, Yahoo! Messenger : http://fr.messenger.yahoo.com