From owner-chemistry@ccl.net Wed Dec 19 08:32:01 2007 From: "Andrea Ciccioli andrea.ciccioli+*+uniroma1.it" To: CCL Subject: CCL:G: "Low frequencies" in Gaussian Freq Jobs Message-Id: <-35882-071219064047-5508-dRlXl89DXBtL303uPW76oA- -server.ccl.net> X-Original-From: "Andrea Ciccioli" Date: Wed, 19 Dec 2007 06:40:42 -0500 Sent to CCL by: "Andrea Ciccioli" [andrea.ciccioli_-_uniroma1.it] Dear friends, it is commonly asserted in textbooks and software manuals that the obvious test to recognize minima in PES among stationary points is that the vibrational frequencies have to be real. However, I wonder if besides this criterium one should also check carefully the values of the frequencies reported as "Low frequencies" in Gaussian outputs (just before the list of Harmonic frequencies). These are the "frequencies" actually corresponding to translations and rotations, and they should be ideally equal to zero, and indeed in many cases they are very low. However, it happens not seldom to me, e.g. for triatomic species containing heavy elements such as transition metals, to obtain outputs where, although the harmonic vibrational frequencies are all real (positive numbers in the Gaussian output), ie the structure should be a minimum, nevertheless one or two "Low Frequencies" are not that low. Furthermore, they are in general both positive and negative. For example, low frequencies as high as +/- 10 to 40 cm-1 are obtained. Moreover, these values are apparently larger for analytic second-derivative frequency calculations than for numerical calculations (I use DFT methods). As far as you know, these relatively high values of the "Low Frequencies" can indicate that the calculated structure is not a true minimum, in spite of having real harmonic frequencies ? What could be a reasonable criterium to consider the "Low frequencies" small enough to be sure that the stationary point is a true minimum ? Has anyone some suggestions/indications to give me ? Thanks to all, and season's greetings. Andrea Ciccioli University of Rome (ITALY) Sapienza From owner-chemistry@ccl.net Wed Dec 19 09:07:00 2007 From: "Agesilaos George Hantzis ahatz^^^chemistry.upatras.gr" To: CCL Subject: CCL:G: A strange finding about G98 Message-Id: <-35883-071219075119-1954-IKE4k+9FV/l1Yp0zDj91Qw*o*server.ccl.net> X-Original-From: "Agesilaos George Hantzis" Date: Wed, 19 Dec 2007 07:51:16 -0500 Sent to CCL by: "Agesilaos George Hantzis" [ahatz-,-chemistry.upatras.gr] Dear CCLers I am running a CCSD(T) single point calculation with G98 set of programs. I have partioned the RWF file into six sections and used %mem=1500mb. The job started and eventually reached a point where all partitions were filled (2gb each) and the job failed. I tried %mem=1000mb and the job is running up to now (it hasn't finished yet). My system has 3GB of memory. I wonder if anyone had similar experiences using the program. Also i would like to ask if there is some connection between the %mem option and the maximum partioning of the RWF file. Thank you in advance From owner-chemistry@ccl.net Wed Dec 19 12:50:00 2007 From: "Oscar Odio Chacón odio[#]imre.oc.uh.cu" To: CCL Subject: CCL:G: Problems finding TS Message-Id: <-35884-071218175816-7747-E9O266xzYOANkHnwB4ppQg,+,server.ccl.net> X-Original-From: Oscar Odio Chacón Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 18 Dec 2007 17:05:04 -0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Oscar Odio Chacón [odio---imre.oc.uh.cu] Hello, CCLers: I´m trying to calculate the transition state of a radical addition reaction to an olefin using Gaussian 98. The problem arises because the output negative frequency does not correspond with vibrational motion of the bond formed in the product, but corresponds to a motion associated with a methyl group near the radical. So, what can I do? Remove the methyl group? In my opinion, this methyl group would have influence in the transition state energy. The overall system contains 47 atoms, 415 basis functions, 707 primitive gaussians, 70 alpha electrons, 69 beta electrons. The command line was # b3lyp/6-31g(d,p) opt=(modredundant, TS, noeigentest) freq. Thanks in advance. Oscar Odio -- Lic. Oscar Odio Chacón Laboratorio de Polímeros IMRE "Al mundo nuevo corresponde la Universidad nueva" UNIVERSIDAD DE LA HABANA 280 aniversario Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http://www.universidad2008.cu From owner-chemistry@ccl.net Wed Dec 19 15:53:00 2007 From: "Dave . ccl_list~~giantscience.com" To: CCL Subject: CCL: Setting up new (academic) research lab; software purchase questions Message-Id: <-35885-071219132918-25219-UWwntegxcKxwd3/ul/YCyw_-_server.ccl.net> X-Original-From: "Dave ." Date: Wed, 19 Dec 2007 13:29:14 -0500 Sent to CCL by: "Dave ." [ccl_list,,giantscience.com] I'm in the process of setting up a new modeling research lab at MIT (academic lab). I'm trying to put together a budget for modeling software we'll want to purchase for the coming year. We will be part of a drug design effort, so we'll be doing the standard stuff associated with such an effort (visualization of ligands and proteins, docking, scoring [binding, ADME], etc.) We expect to have a lot of compounds/data flowing through via library screening. The software we already have access to (free to us) includes the MOE package, Pipeline Pilot, and the complete CambridgeSoft suite. The question is: What software should I budget purchasing? I was considering, in particular, the Schrodinger stuff. The quote I got was $11,500/year for a single license for their suite, or $5000/year for 20 "tokens", that will allow me to run run 3-4 of their programs simultaneously. Any suggestions/comments on this pricing and which option is preferable? I'd like to bring in Insight, because that's the program I've used for visualization for a long time, but I've heard that Accelrys' pricing is not too academic friendly. Alternatively, I can bring in the academic (nearly) freeware: Amber, Dock, Modeler, PyMol, etc. Of course, then you don't get the nice(r) integration of stuff like Schrodinger. I'm open to hearing alternatives, yes/nos, etc. We can definitely put money in the budget for modeling software. I just don't want to toss money into the street unnecessarily. From owner-chemistry@ccl.net Wed Dec 19 16:28:00 2007 From: "Debellis Anthony CE US anthony.debellis,,ciba.com" To: CCL Subject: CCL:G: Problems finding TS Message-Id: <-35886-071219141333-5396-NXiF5WPR9HXwNjj9BqvbrQ|*|server.ccl.net> X-Original-From: Debellis Anthony CE US Content-Class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 19 Dec 2007 13:43:47 -0500 MIME-Version: 1.0 Sent to CCL by: Debellis Anthony CE US [anthony.debellis=-=ciba.com] Hello Oscar, One possibility would be to locate the transition state with the methyl = group removed, then add back the methyl to the resulting TS structure = followed by a further TS optimization. Anthony DeBellis Ciba -----Original Message----- > From: owner-chemistry*|*ccl.net [mailto:owner-chemistry*|*ccl.net]=20 Sent: Tuesday, December 18, 2007 12:05 PM To: Debellis Anthony CE US Subject: CCL:G: Problems finding TS Sent to CCL by: Oscar Odio Chac=F3n [odio---imre.oc.uh.cu] Hello, CCLers: I=B4m trying to calculate the transition state of a radical addition = reaction to an olefin using Gaussian 98. The problem arises because the = output negative frequency does not correspond with vibrational motion of = the bond formed in the product, but corresponds to a motion associated = with a methyl group near the radical. So, what can I do? =20 Remove the methyl group? In my opinion, this methyl group would have influence in the transition = state energy. The overall system contains 47 atoms, 415 basis functions, 707 primitive = gaussians, 70 alpha electrons, 69 beta electrons. The command line was = # b3lyp/6-31g(d,p) opt=3D(modredundant, TS, noeigentest) freq. Thanks in advance. Oscar Odio -- Lic. Oscar Odio Chac=F3n Laboratorio de Pol=EDmeros IMRE "Al mundo nuevo corresponde la Universidad nueva" UNIVERSIDAD DE LA HABANA 280 aniversario Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http://www.universidad2008.cu -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Dec 19 20:14:01 2007 From: "Guanna Li gnli:_:dicp.ac.cn" To: CCL Subject: CCL: Problems finding TS Message-Id: <-35887-071219200103-450-ju4MYHdnXHJY6q6UkB2TYQ * server.ccl.net> X-Original-From: "Guanna Li" Content-Transfer-Encoding: base64 Content-Type: text/plain; charset="gb2312" Date: Thu, 20 Dec 2007 09:00:50 +0800 Mime-Version: 1.0 Sent to CCL by: "Guanna Li" [gnli[A]dicp.ac.cn] RGVhciBPZGlvo6wNCiAgSXQgc2VlbXMgbGlrZSB0aGUgdHMgc3RhdGUgeW91IGNhbGN1bGF0ZSBp cyBub3QgdGhlIHJlYWwgcmVhY3Rpb24gdHJhbnNpdGlvbiBzdGF0ZS4geW91IGNhbiB0cnkgUVNU Mi4NCg0KDQotLS0tLS0tLS0tLS0tLS0tLS0JCQkJIA0KR3Vhbm5hIExpDQoyMDA3LTEyLTIwDQpC ZXN0IHdpc2hlcyAgIA0KU3RhdGUgS2V5IExhYm9yYXRvcnkgb2YgQ2F0YWx5c2lzDQpEYWxpYW4g SW5zdGl0dXRlIG9mIENoZW1pY2FsIFBoeXNpY3MNCkNoaW5lc2UgQWNhZGVteSBvZiBTY2llbmNl cw0KIA0KNDU3IFpob25nc2hhbiBSb2FkLCBEYWxpYW4gMTE2MDIzLCBDaGluYQ0KIA0KVGVsOiAr ODYtNDExLTg0MzcgOTMwMg0KRW1haWw6IGdubGlAZGljcC5hYy5jbg0KDQotLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tDQq3orz+yMuj uk9zY2FyIE9kaW8gQ2hhY/NuIG9kaW9bI11pbXJlLm9jLnVoLmN1DQq3osvNyNXG2qO6MjAwNy0x Mi0yMCAwMjoxNjozMA0KytW8/sjLo7pMaSwgR3Vhbm5hIC1pZCMzZHYtDQqzrcvNo7oNCtb3zOKj ukNDTDpHOiBQcm9ibGVtcyBmaW5kaW5nIFRTDQoNCg0KU2VudCB0byBDQ0wgYnk6IE9zY2FyIE9k aW8gQ2hhY/NuIFtvZGlvLS0taW1yZS5vYy51aC5jdV0NCg0KSGVsbG8sIENDTGVyczoNCkm0bSB0 cnlpbmcgdG8gY2FsY3VsYXRlIHRoZSB0cmFuc2l0aW9uIHN0YXRlIG9mIGEgcmFkaWNhbA0KYWRk aXRpb24gcmVhY3Rpb24gdG8gYW4gb2xlZmluIHVzaW5nIEdhdXNzaWFuIDk4LiBUaGUgcHJvYmxl bSBhcmlzZXMNCmJlY2F1c2UgdGhlIG91dHB1dCBuZWdhdGl2ZSBmcmVxdWVuY3kgZG9lcyBub3Qg Y29ycmVzcG9uZCB3aXRoIHZpYnJhdGlvbmFsDQptb3Rpb24gb2YgdGhlIGJvbmQgZm9ybWVkIGlu IHRoZSBwcm9kdWN0LCBidXQgY29ycmVzcG9uZHMgdG8gYSBtb3Rpb24NCmFzc29jaWF0ZWQgd2l0 aCBhIG1ldGh5bCBncm91cCBuZWFyIHRoZSByYWRpY2FsLiBTbywgd2hhdCBjYW4gSSBkbz8gIA0K UmVtb3ZlIHRoZSBtZXRoeWwgZ3JvdXA/DQpJbiBteSBvcGluaW9uLCB0aGlzIG1ldGh5bCBncm91 cCB3b3VsZCBoYXZlIGluZmx1ZW5jZSBpbiB0aGUgdHJhbnNpdGlvbiANCnN0YXRlIGVuZXJneS4N ClRoZSBvdmVyYWxsIHN5c3RlbSBjb250YWlucyA0NyBhdG9tcywgNDE1IGJhc2lzIGZ1bmN0aW9u cywgNzA3IHByaW1pdGl2ZSANCmdhdXNzaWFucywgNzAgYWxwaGEgZWxlY3Ryb25zLCA2OSBiZXRh IGVsZWN0cm9ucy4gVGhlIGNvbW1hbmQgbGluZSB3YXMgICMNCmIzbHlwLzYtMzFnKGQscCkgb3B0 PShtb2RyZWR1bmRhbnQsIFRTLCBub2VpZ2VudGVzdCkgZnJlcS4NClRoYW5rcyBpbiBhZHZhbmNl Lg0KT3NjYXIgT2Rpbw0KDQoNCg0KDQoNCi0tIA0KTGljLiBPc2NhciBPZGlvIENoYWPzbg0KTGFi b3JhdG9yaW8gZGUgUG9s7W1lcm9zDQpJTVJFDQoNCg0KDQoiQWwgbXVuZG8gbnVldm8gY29ycmVz cG9uZGUgbGEgVW5pdmVyc2lkYWQgbnVldmEiDQpVTklWRVJTSURBRCBERSBMQSBIQUJBTkENCjI4 MCBhbml2ZXJzYXJpbw0KUGFydGljaXBlIGVuIFVuaXZlcnNpZGFkIDIwMDggZGVsIDExIGFsIDE1 IGRlIGZlYnJlcm8gZGVsIDIwMDguDQpQYWxhY2lvIGRlIENvbnZlbmNpb25lcy4gTGEgSGFiYW5h LiBDdWJhLg0KaHR0cDovL3d3dy51bml2ZXJzaWRhZDIwMDguY3UNCg0KDQoNCi09IFRoaXMgaXMg YXV0b21hdGljYWxseSBhZGRlZCB0byBlYWNoIG1lc3NhZ2UgYnkgdGhlIG1haWxpbmcgc2NyaXB0 ID0tDQpUbyByZWNvdmVyIHRoZSBlbWFpbCBhZGRyZXNzIG9mIHRoZSBhdXRob3Igb2YgdGhlIG1l c3NhZ2UsIHBsZWFzZSBjaGFuZ2UNCnRoZSBzdHJhbmdlIGNoYXJhY3RlcnMgb24gdGhlIHRvcCBs aW5lIHRvIHRoZSBAIHNpZ24uIFlvdSBjYW4gYWxzbw0KbG9vayB1cCB0aGUgWC1PcmlnaW5hbC1G cm9tOiBsaW5lIGluIHRoZSBtYWlsIGhlYWRlci4NCg0KRS1tYWlsIHRvIHN1YnNjcmliZXJzOiBD SEVNSVNUUllAY2NsLm5ldCBvciB1c2U6DQogICAgICBodHRwOi8vd3d3LmNjbC5uZXQvY2dpLWJp bi9jY2wvc2VuZF9jY2xfbWVzc2FnZQ0KDQpFLW1haWwgdG8gYWRtaW5pc3RyYXRvcnM6IENIRU1J U1RSWS1SRVFVRVNUQGNjbC5uZXQgb3IgdXNlDQogICAgICBodHRwOi8vd3d3LmNjbC5uZXQvY2dp LWJpbi9jY2wvc2VuZF9jY2xfbWVzc2FnZQ0KDQpTdWJzY3JpYmUvVW5zdWJzY3JpYmU6IA0KICAg ICAgaHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9zdWJfdW5zdWIuc2h0bWwNCg0KQmVmb3Jl IHBvc3RpbmcsIGNoZWNrIHdhaXQgdGltZSBhdDogaHR0cDovL3d3dy5jY2wubmV0DQoNCkpvYjog aHR0cDovL3d3dy5jY2wubmV0L2pvYnMgDQpDb25mZXJlbmNlczogaHR0cDovL3NlcnZlci5jY2wu bmV0L2NoZW1pc3RyeS9hbm5vdW5jZW1lbnRzL2NvbmZlcmVuY2VzLw0KDQpTZWFyY2ggTWVzc2Fn ZXM6IGh0dHA6Ly93d3cuY2NsLm5ldC9odGRpZyAgKGxvZ2luOiBjY2wsIFBhc3N3b3JkOiBzZWFy Y2gpDQoNCklmIHlvdXIgbWFpbCBib3VuY2VzIGZyb20gQ0NMIHdpdGggNS43LjEgZXJyb3IsIGNo ZWNrOg0KICAgICAgaHR0cDovL3d3dy5jY2wubmV0L3NwYW1tZXJzLnR4dA0KDQpSVEZJOiBodHRw Oi8vd3d3LmNjbC5uZXQvY2hlbWlzdHJ5L2Fib3V0Y2NsL2luc3RydWN0aW9ucy8NCg0KDQoNCg0K LS0gDQpObyB2aXJ1cyBmb3VuZCBpbiB0aGlzIGluY29taW5nIG1lc3NhZ2UuDQpDaGVja2VkIGJ5 IEFWRyBGcmVlIEVkaXRpb24uIA0KVmVyc2lvbjogNy41LjUwMyAvIFZpcnVzIERhdGFiYXNlOiAy NjkuMTcuNC8xMTg5IC0gUmVsZWFzZSBEYXRlOiAyMDA3LTEyLTE4IDIxOjQwDQoNCi4NCg==