From chemistry-request@ccl.net Wed Apr 7 19:29:58 2004 Received: from ms-smtp-02-eri0.ohiordc.rr.com (ms-smtp-02-smtplb.ohiordc.rr.com [65.24.5.136]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i380TwjR005280 for ; Wed, 7 Apr 2004 19:29:58 -0500 Received: from HOME (dhcp024-208-195-225.indy.rr.com [24.208.195.225]) by ms-smtp-02-eri0.ohiordc.rr.com (8.12.10/8.12.7) with SMTP id i380Txf4007619 for ; Wed, 7 Apr 2004 20:30:04 -0400 (EDT) Message-ID: <000c01c41d00$a23abb20$0100a8c0@HOME> From: "Q" To: Subject: CCL: calculate accessible surface area for an occluded cavity Date: Wed, 7 Apr 2004 19:29:58 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C41CD6.B6A7DD10" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Virus-Scanned: Symantec AntiVirus Scan Engine This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C41CD6.B6A7DD10 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All, I have a protein with an internal cavity that has no access to the = outside solvent. I would like to calculate the accessible surface area = of the residues inside the cavity to see how accessible they are to the = cavity. How can I do this or what programs could help to do it? How = about NACCESS? Thanks for any input. Qin ------=_NextPart_000_0009_01C41CD6.B6A7DD10 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear All,

I have a protein with an internal = cavity that=20 has no access to the outside solvent. I would like to calculate the = accessible=20 surface area of the residues inside the cavity to see how accessible = they are to=20 the cavity. How can I do this or what programs could help to do it? How = about=20 NACCESS? Thanks for any input.

Qin

------=_NextPart_000_0009_01C41CD6.B6A7DD10-- From chemistry-request@ccl.net Wed Apr 7 21:26:01 2004 Received: from mb1i1.ns.pitt.edu (mb1i1.ns.pitt.edu [136.142.185.161]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i382Q0jR010235 for ; Wed, 7 Apr 2004 21:26:01 -0500 Received: from CONVERSION-DAEMON by pitt.edu (PMDF V5.2-32 #41462) id <01L8NXVDAFSG0017XC_at_mb1i1.ns.pitt.edu> for chemistry_at_ccl.net; Wed, 7 Apr 2004 22:24:43 EDT Received: from visual1.chem.pitt.edu ([136.142.109.16]) by pitt.edu (PMDF V5.2-32 #41462) with ESMTP id <01L8NXVAPWFM004IOI_at_mb1i1.ns.pitt.edu>; Wed, 07 Apr 2004 22:24:41 -0400 (EDT) Date: Wed, 07 Apr 2004 22:24:35 -0400 From: Kadir Diri Subject: Re: CCL:Calculate N2 with different basis sets In-reply-to: <000c01c41cd2$4acbda00$3db15ba5@yubopclab> To: Yubo Fan Cc: chemistry_at_ccl.net Message-id: <4074B7E3.9080901_at_visual1.chem.pitt.edu> MIME-version: 1.0 Content-type: multipart/alternative; boundary="Boundary_(ID_/tPwk+g7EnXeYJNxrxku5w)" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en References: <000c01c41cd2$4acbda00$3db15ba5@yubopclab> This is a multi-part message in MIME format. --Boundary_(ID_/tPwk+g7EnXeYJNxrxku5w) Content-type: text/plain; charset=us-ascii; format=flowed Content-transfer-encoding: 7bit Hi! You didn`t tell absolutely anything about the error you get, the method you use and the type of the calculation. Gaussian shouldn`t have any problems with such simple cases. It is a good idea to mention all of the above plus the operating system when asking about problems with software. About the input, there should be nothing tricky, since this is a fairly simple molecule and all "defaults" will work. One of the simplest inputs you can give is below. Regards, kadir %mem=?mb //put available memory// #P mp2/6-31g* opt test ...............blank line title card ...............blank line 0 1 N N 1 d ...............blank line d 1.0 ..................blank line Yubo Fan wrote: > Hi, > > I tried to use different basis sets to calculate N2 molecule but > failed. How can I set the Gaussian 03 input file to run this type of > homoatomic molecules? Thanks. > > Sincerely, > > Yubo --Boundary_(ID_/tPwk+g7EnXeYJNxrxku5w) Content-type: text/html; charset=us-ascii Content-transfer-encoding: 7bit Hi! You didn`t tell absolutely anything about the error you get, the method you use and the type of the calculation. Gaussian shouldn`t have any problems with such simple cases. It is a good idea to mention all of the above plus the operating system when asking about problems with software.
About the input, there should be nothing tricky, since this is a fairly simple molecule and all "defaults" will work. One of the simplest inputs you can give is below.
Regards,
kadir

%mem=?mb              //put available memory//
#P mp2/6-31g* opt test
...............blank line
title card
...............blank line
0 1
N
N                  1              d
...............blank line
   d             1.0
..................blank line

Yubo Fan wrote:

Hi,

I tried to use different basis sets to calculate N2 molecule but failed. How can I set the Gaussian 03 input file to run this type of homoatomic molecules? Thanks.

Sincerely,

Yubo

--Boundary_(ID_/tPwk+g7EnXeYJNxrxku5w)-- From chemistry-request@ccl.net Thu Apr 8 04:01:39 2004 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3891cjR002785 for ; Thu, 8 Apr 2004 04:01:38 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.10/jtpda-5.4) with ESMTP id i3891jIu005054 for ; Thu, 8 Apr 2004 11:01:45 +0200 (CEST) X-Ids: 164 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id i3891cV2508860; Thu, 8 Apr 2004 11:01:38 +0200 (MEST) Date: Thu, 8 Apr 2004 11:01:38 +0200 (MEST) From: Michel Petitjean Message-Id: <200404080901.i3891cV2508860-.at.-ds10.itodys.jussieu.fr> To: chemistry-.at.-ccl.net Subject: CCL: Re: calculate accessible surface area for an occluded cavity X-Miltered: at shiva.jussieu.fr with ID 407514F9.001 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr To: Subj: CCL: Re: calculate accessible surface area for an occluded cavity Dear Qin, May I suggest two ways. I assume that you know which residues are on the boundary on the cavity. Using adequate radii, the SAS can be computed either analytically, or by Monte-Carlo (faster, but less accurate), with the freeware ASV: binaries and documentation with reference in: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV Also, if you have a roughly convex cavity (e.g. the convex hull of the alpha-carbons bounding the cavity), you can get the surface of the hull (and its generalized radius and diameter), with the free ware RADI: binaries and documentation with reference in: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI Michel Petitjean, Email: petitjean-.at.-itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean-.at.-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.html .................................................................. > From owner-chemistry-.at.-ccl.net Thu Apr 8 08:19:56 2004 From: "Q" To: Subject: CCL:calculate accessible surface area for an occluded cavity Date: Wed, 7 Apr 2004 19:29:58 -0500 Dear All, I have a protein with an internal cavity that has no access to the = outside solvent. I would like to calculate the accessible surface area = of the residues inside the cavity to see how accessible they are to the = cavity. How can I do this or what programs could help to do it? How = about NACCESS? Thanks for any input. Qin From chemistry-request@ccl.net Thu Apr 8 09:14:59 2004 Received: from SGOFSMTP01.nac.ppg.com (smtpout.ppg.com [141.189.251.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i38EExjR018043 for ; Thu, 8 Apr 2004 09:14:59 -0500 Received: from SGOFUSR25.nac.ppg.com ([10.49.120.8]) by SGOFSMTP01.nac.ppg.com with Microsoft SMTPSVC(5.0.2195.5329); Thu, 8 Apr 2004 10:03:13 -0400 content-class: urn:content-classes:message Subject: Enforcing symmetry within G98 Date: Thu, 8 Apr 2004 10:03:12 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Enforcing symmetry within G98 X-MimeOLE: Produced By Microsoft Exchange V6.0.6375.0 Thread-Index: AcQdcjshm5bM4s/TTACvxEp6PyRjHQ== From: "Makowski, Mike" To: X-OriginalArrivalTime: 08 Apr 2004 14:03:13.0842 (UTC) FILETIME=[3BB52120:01C41D72] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i38EF0jR018044 I am performing some geometry optimizations in vacuuo on some large organo-metallic complexes with C3 or higher symmetry. My problem is that I cannot find a way to enforce this symmetry during the optimization routine. Is there a set of keywords that can be employed to prevent G98 from defaulting to C1 symmetry or to enforce a particular symmetry? The structures we get using C1 optimizations are "reasonable", but clearly should be much better. Based on the resultant bond lengths and angles the symmetry is certainly not obeyed. Any help would be appreciated. -Mike Michael P. Makowski, Ph.D. Group Leader Applied Scientific Computing PPG Industries R&D 412-492-5359 (ph) 412-492-5577 (fax) makowski~at~ppg.com From chemistry-request@ccl.net Thu Apr 8 08:37:21 2004 Received: from up.univ-mrs.fr (mailup.univ-mrs.fr [147.94.113.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i38DbKjR016327 for ; Thu, 8 Apr 2004 08:37:21 -0500 Received: from localhost (localhost [127.0.0.1]) by up.univ-mrs.fr (Postfix) with ESMTP id 8AAAE1B424B for ; Thu, 8 Apr 2004 15:37:20 +0200 (CEST) Received: from up.univ-mrs.fr ([127.0.0.1]) by localhost (mailup.univ-mrs.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 502953-02 for ; Thu, 8 Apr 2004 15:37:20 +0200 (CEST) Received: from up.univ-mrs.fr (unknown [147.94.185.160]) by up.univ-mrs.fr (Postfix) with ESMTP id 3C3A3188D1D for ; Thu, 8 Apr 2004 15:37:20 +0200 (CEST) Message-ID: <4075546A.4010700~at~up.univ-mrs.fr> Date: Thu, 08 Apr 2004 15:32:26 +0200 From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Organization: LCTMM User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr-FR; rv:1.6) Gecko/20040113 X-Accept-Language: fr-fr, en-us, en MIME-Version: 1.0 To: chemistry~at~ccl.net Subject: G03: relaxed scan at the CCSD(T) level Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new at up.univ-mrs.fr Hi, Does anyone found a way to perform a relaxed PES scan using a method for which only numerical gradients are available ? I tried with opt=modredundant or opt=z-matrix, but it does not work. Actually the link used for this kind of geometry optimization is the 114 one, i.e. the EF one. Regards, Nicolas Ferri From chemistry-request@ccl.net Thu Apr 8 03:32:17 2004 Received: from duras.rz-berlin.mpg.de (duras.RZ-Berlin.MPG.DE [141.14.130.154]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i388WGjR032705 for ; Thu, 8 Apr 2004 03:32:17 -0500 Received: from localhost (unknown [127.0.0.1]) by duras.rz-berlin.mpg.de (Postfix) with ESMTP id 1712EED1B4; Thu, 8 Apr 2004 10:32:22 +0200 (CEST) Received: from duras.rz-berlin.mpg.de ([127.0.0.1]) by localhost (duras [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 66388-02; Thu, 8 Apr 2004 10:32:19 +0200 (CEST) Received: from [141.14.151.188] (MacGvH.rz-berlin.mpg.de [141.14.151.188]) by duras.rz-berlin.mpg.de (Postfix) with ESMTP id 59326EBC19; Thu, 8 Apr 2004 10:32:19 +0200 (CEST) Mime-Version: 1.0 X-Sender: helden~at~imap.rz-berlin.mpg.de (Unverified) Message-Id: In-Reply-To: <3130b530f280.30f2803130b5~at~uni-bielefeld.de> References: <3130b530f280.30f2803130b5~at~uni-bielefeld.de> Date: Thu, 8 Apr 2004 10:32:20 +0200 To: Andreas Serr , chemistry~at~ccl.net From: Gert von Helden Subject: Re: CCL:gaussian 03 on macintosh Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-Virus-Scanned: by amavisd-new (PP&B) at duras dear all, MacOSX is just another regular UNIX and one can compile the standard g03 source code on that machine (and optimize for the G5!). I did so and it runs very fast. On a typical DFT job, it is 2-3 times (yes, that much!) faster than on a Xeon (comparing a single 2 GHz Xeon CPU to a single 2 GHz G5 CPU). For visualization, I use mostly viewmol, an excellent program for looking at molecules, vibrations, orbitals.... Added advantage: its free. There are a couple of points to consider if you want to compile g03 on MacOSX: I used the IBM xlf compiler (8.1 beta). The final version of the compiler is available now, I am about to order that one. It order to compile, you need a UNIX filesystem partition on the disk where g03 is compiling, as hfs and hfs+ are not really case sensitive and in the preprocessor stage of the compilation (cpp), it needs to distinguish between xxxx.F and xxxx.f. The makefile is a hybrid of the rs6k.make and the linux makefile. I also added a few lines of fortran code and slightly modified some c source files (only on some files in the bsd subdir). Of course one has to keep in mind that the byteorder on a PowerPC is different from Intel and that, although the CPU is 64 bit, MacOSX is not (no support for 8 byte pointers). I also used the Apple BLAS (veclib). The resulting code runs very well, 16 GB scratchfiles are no problem (no need to segment into 2 GB chunks). Bigger scratchfiles do not work, I guess the reason are the 4 byte pointers. I tried to compile it for 2 CPUs (using openMP). That did not work and since I don't care, I gave up quickly. My feeling is that after spending some time, that would work as well. Good luck, Gert At 16:53 +0200 7/4/04, Andreas Serr wrote: >Dear all, > >we are considering using Gaussian 03 on a Mac OS X >system. Has anybody experience in that field? In >particular: > >- G03M is not optimised for Mac G5 architecture, so >does it make sense to run it on G5 rather than on G4? > >- is GaussView M working fine with G5 computers? > >- does anyone have experience/benchmark tests for >Gaussian running on Mac (G5/G4/...) in comparison >with Gaussian on Intel Xeon-dual process. @ 2 GHz >(Linux system) > >Regards, >Andy > >andreas.serr~at~uni-bielefeld.de > > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY~at~ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST~at~ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow~at~nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- ------------------------------------- Gert von Helden Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin tel.: +49-30-8413 5615 fax: +49-30-8413 5603 From chemistry-request@ccl.net Thu Apr 8 05:44:06 2004 Received: from zmail.pt (smtp.zmail.pt [81.92.196.136]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i38Ai5jR008285 for ; Thu, 8 Apr 2004 05:44:06 -0500 Received: from WorldClient by zmail.pt (MDaemon.PRO.v6.8.4.R) with ESMTP id 9-md50000000004.tmp for ; Thu, 08 Apr 2004 11:42:24 +0100 Received: from [194.117.40.12] via WorldClient with HTTP; Thu, 08 Apr 2004 11:42:24 +0100 Date: Thu, 08 Apr 2004 11:42:24 +0100 From: "=?iso-8859-1?Q?Gon=E7alo?= Deira Justino" To: chemistry|at|ccl.net Subject: molecular radius MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Message-ID: X-Mailer: ZMAIL.PT 6.8.4 X-Spam-Processed: smtp.zmail.pt, Thu, 08 Apr 2004 11:42:24 +0100 (not processed: spam filter disabled) X-Return-Path: goncalo.justino|at|zmail.pt X-MDaemon-Deliver-To: chemistry|at|ccl.net Reply-To: goncalo.justino|at|zmail.pt hi all does anyone know a fast way to compute te radius of small solutes (2 to 5 atoms) - or any extensive tables that could cover these? thanks Gongalo Justino From chemistry-request@ccl.net Thu Apr 8 09:21:42 2004 Received: from kaist.ac.kr (webmail.kaist.ac.kr [143.248.5.130]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i38ELejR018237 for ; Thu, 8 Apr 2004 09:21:41 -0500 Received: (qmail 16842 invoked from network); 8 Apr 2004 23:21:37 +0900(KST) Received: from unknown (HELO ilsun) (143.248.37.227) by 0 with SMTP; 8 Apr 2004 23:21:37 +0900(KST) Message-ID: <001201c41d74$d3338f80$e325f88f@ilsun> From: "Kwanyong Seo" To: "CCL" Subject: Suitable basis set for organometallic compound Date: Thu, 8 Apr 2004 23:21:46 +0900 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000F_01C41DC0.43119A90" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_000_000F_01C41DC0.43119A90 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: base64 RGVhciBDQ0xlcnMNCg0KSSBoYXZlIGZlbHQgIGRpZmZpY3VsdHkgdG8gc2VsZWN0IGJhc2lzIHNl dCBmb3IgY2FsY3VsYXRpb24gb2Ygb3JnYW5vbWV0YWxsaWMgY29tcG91bmQuDQpBbHRob3VnaCB3 ZSBub3JtYWxseSB1c2UgNi0zMUcgYmFzaXMgc2V0IGZvciBnZW5lcmFsIGFiLWluaXRpbyBjYWxj dWxhdGlvbnMsIA0KdGhpcyBiYXNpcyBzZXQgY2FuJ3QgYmUgYXBwbGllZCB0byBoZWF2eSBlbGVt ZW50cy4gDQoNCkFjdHVhbGx5IEkgY2FuIHVzZSAzLTIxRyBiYXNpcyBzZXQgaW5zdGVhZCBvZiA2 LTMxRyBiYXNpcyBzZXQuIA0KSG93ZXZlciwgSSB3YW50IHRvIHBlcmZvcm0gdGhlIG1vcmUgYWNj dXJhdGUgY2FsY3VsYXRpb24gd2l0aCBzdWl0YWJsZSBiYXNpcyBzZXQuDQoNClNvLCBJIGhhdmUg dHdvIHF1ZXN0aW9ucy4NCg0KMS4gSWYgd2UgdXNlIHR3byB0eXBlcyBvZiBiYXNpcyBzZXQgaW4g b25lIGNhbGN1bGF0aW9uLiBIb3cgY2FuIHdlIHdyaXRlIHRoZSBiYXNpcyBzZXQgaW4NCiAgIEcw MyBpbnB1dC4gKEZvciBleGFtcGxlOiBXaGVuIHdlIGNhbGN1bGF0ZSB0aGUgRmUoQ08pNSBtb2xl Y3VsZSwgd2UgdXNlIDYtMzFHIGJhc2lzIHNldCBmb3IgY2FyYm9uIGFuZA0KICAgT3h5Z2VuIGF0 b20sIGFuZCB3ZSB1c2UgRUNQIGJhc2lzIHNldCBmb3IgaXJvbiBhdG9tKQ0KDQoyLiBXaWxsIHlv dSByZWNvbW1lbmQgc3VpdGFibGUgYmFzaXMgc2V0IGluIEcwMyBjYWxjdWx0aW9uIHdoaWNoIGNv bnRhaW5zIG1ldGFsIG9yIGhlYXZ5IGVsZW1lbnQ/DQoNClJlZ2FyZHMsDQpLd2FueW9uZy4NCg0K DQorKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysN Ckt3YW55b25nIFNlbyA6IChFLW1haWwpIGJsdWVfc2t5QGthaXN0LmFjLmtyIChmaXJzdCkNCiAg ICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICBjdXBpZEBhbGthbGkua2Fpc3Qu YWMua3INCiAgICAgICAgICAgICAgICAgICAgICAgICAgICAoTVNOKSAgY2hlbWlzdF9za3lAaG90 bWFpbC5jb20NCiAgICAgICAgICAgICAgICAgICAgICAgICAgICAoSG9tZSkgaHR0cDovL2Fsa2Fs aS5rYWlzdC5hYy5rci9za3kuaHRtbA0KUGguIEQgY2FuZGlkYXRlDQpEZXBhcnRtZW50IG9mIENo ZW1pc3RyeQ0KS29yZWEgQWR2YW5jZWQgSW5zdGl0dXRlIG9mIFNjaWVuY2UgJiBUZWNobm9sb2d5 DQozNzMtMSwgR3VzZW9uZy1kb25nLCBZdXNlb25nLWd1LA0KVGFlam9uLCBSZXB1YmxpYyBvZiBL b3JlYSANCjMwNS03MDENCisrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysr KysrKysrKysrKysrKw0K ------=_NextPart_000_000F_01C41DC0.43119A90 Content-Type: text/html; 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Thu, 8 Apr 2004 09:11:08 -0500 Received: from fujitsu2.fujitsu.com (localhost [127.0.0.1]) by fujitsu2.fujitsu.com (8.12.10/8.12.9) with ESMTP id i38EBGeq024190 for ; Thu, 8 Apr 2004 07:11:16 -0700 (PDT) Received: from fnanic.fujitsu.com ([133.164.253.2]) by fujitsu2.fujitsu.com (8.12.10/8.12.9) with ESMTP id i38EBGYP024159; Thu, 8 Apr 2004 07:11:16 -0700 (PDT) Received: from cachemai2.fnanic.fujitsu.com (localhost [127.0.0.1]) by fnanic.fujitsu.com (8.12.11/8.12.11) with ESMTP id i38EBEbU000467; Thu, 8 Apr 2004 07:11:14 -0700 (PDT) Received: from DAVEG-LIFEBOOK.cachesoftware.com (localhost [127.0.0.1]) by cachemai2.fnanic.fujitsu.com (8.12.11/8.12.11) with ESMTP id i38EJffU024631; Thu, 8 Apr 2004 07:19:43 -0700 (PDT) Message-Id: <6.0.3.0.0.20040408070546.01d33828@133.164.253.30> X-Sender: dgallagher@133.164.253.30 (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 6.0.3.0 Date: Thu, 08 Apr 2004 07:11:04 -0700 To: Anatoli Korkin , chemistry|at|ccl.net From: David Gallagher Subject: Re: CCL:Comparison ab initio vs DFT and semi-empirical methods Cc: jlabanow|at|nd.edu In-Reply-To: <20040407223031.87190.qmail|at|web20909.mail.yahoo.com> References: <20040407223031.87190.qmail|at|web20909.mail.yahoo.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Anatoli, The following recent paper compares the accuracy of various semiempirical methods with DFT of over 1,000 compounds. Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation, James J. P. Stewart, J Mol Model (2004) 10:6-12 Regards, David Gallagher At 03:30 PM 4/7/2004, Anatoli Korkin wrote: >Dear Colleagues, > >I will appreciate if you send me refenece(s) of >your, or someone else's paper or review, where >computed properties (desirably many) calculated >with different methods are tabulated for comparison >of the performance of the higher level ab initio >approaches (e.g. CC, MP4, and/or CI) vs DFT and/or >semi-empirical methods. > >I will send a summary to the list, if there is interest. > >Thank you very much for your help and consideration. > >Best regards, >Anatoli Korkin > >__________________________________ >Do you Yahoo!? >Yahoo! Small Business $15K Web Design Giveaway >http://promotions.yahoo.com/design_giveaway/ > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY|at|ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow|at|nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Apr 8 01:20:05 2004 Received: from zeus.ubbcluj.ro (NS1.UBBCluj.Ro [193.231.20.1]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i386K4jR023750 for ; Thu, 8 Apr 2004 01:20:04 -0500 Received: (qmail 66577 invoked by uid 98); 8 Apr 2004 06:20:11 -0000 Received: from vchis=at=phys.ubbcluj.ro by Zeus.UBBCluj.Ro by uid 82 with qmail-scanner-1.20 (clamuko: 0.67. spamassassin: 2.63. Clear:RC:1(193.231.19.53):. Processed in 0.029709 secs); 08 Apr 2004 06:20:11 -0000 X-Qmail-Scanner-Mail-From: vchis=at=phys.ubbcluj.ro via Zeus.UBBCluj.Ro X-Qmail-Scanner: 1.20 (Clear:RC:1(193.231.19.53):. Processed in 0.029709 secs) Received: from unknown (HELO phys.ubbcluj.ro) (193.231.19.53) by zeus.ubbcluj.ro with SMTP; 8 Apr 2004 06:20:11 -0000 Received: from molphy.phys.ubbcluj.ro (molphys.phys.ubbcluj.ro [172.22.21.203]) by phys.ubbcluj.ro (8.12.8/8.12.8) with ESMTP id i386KECZ014819 for ; Thu, 8 Apr 2004 09:20:14 +0300 Message-Id: <5.0.0.25.2.20040408091543.02280f98=at=phys.ubbcluj.ro> X-Sender: vchis=at=phys.ubbcluj.ro X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Thu, 08 Apr 2004 09:19:16 +0300 To: chemistry=at=ccl.net From: Vasile Chis Subject: specifying the connectivity in Gaussian Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Virus-Scanned: clamd / ClamAV version 0.70rc, clamav-milter version 0.70 Dear Colleagues, I am trying to optimize a molecule (with Gaussian) with two charged groups, +NH3 and COO-, respectively. However, during the optimization, one of the amino hydrogen leaves the nitrogen and bound to one of the oxygen atoms of COO group. In order to preserve the two groups I imposed the same bond length for the three NH bonds, but this means a restriction which even if does not led to imaginary frequencies, however the corresponding optimized geometry must be higher in energy than that in which an NH...O hydrogen bond is allowed. The Help of the program says that there is a way of giving a specific connectivity for atoms, however I was not able to solve my problem. I will appreciate very much any help on this topic. Best regards and Happy Easter for everybody! Vasile ------------------------------------------- Dr. Vasile Chis "Babes-Bolyai" University Dept. of Physics Kogalniceanu 1, RO-400084 Cluj-Napoca Romania Tel: +40 (0)264 405300 ext 5153 Fax: +40 (0)264 591906 e-mail: vchis=at=phys.ubbcluj.ro http://www.phys.ubbcluj.ro/~vchis --------------------------------------------- From chemistry-request@ccl.net Thu Apr 8 12:35:21 2004 Received: from web20904.mail.yahoo.com (web20904.mail.yahoo.com [216.136.226.226]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i38HZKjR026569 for ; Thu, 8 Apr 2004 12:35:21 -0500 Message-ID: <20040408173530.46763.qmail{at}web20904.mail.yahoo.com> Received: from [128.227.192.230] by web20904.mail.yahoo.com via HTTP; Thu, 08 Apr 2004 10:35:30 PDT Date: Thu, 8 Apr 2004 10:35:30 -0700 (PDT) From: Anatoli Korkin Subject: SUMMARY: ab initio vs DFT vs semi-empirical methods To: chemistry{at}ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii > Dear Colleagues, > > I will appreciate if you send me reference(s) of > your, or someone else's paper or review, where > computed properties (desirably many) calculated > with different methods are tabulated for comparison > of the performance of the higher level ab initio > approaches (e.g. CC, MP4, and/or CI) vs DFT and/or > semi-empirical methods. > > I will send a summary to the list, if there is interest. > > Thank you very much for your help and consideration. Dear Colleagues and Friends, Thank you very much for your help with references and copies of the papers and also for an opportunity to have some follow up chat with a few friends. We all move around and dive and surface once in a while :-) Please, find below a summary of the answers that I received, so far. Following the advice from Jan Labanowski, I also encovered a few references in QCLD, which is very useful data base for computational chemists (I am not selling it! :-) Here they are: Theochem, 505 (2000) 289; Theochem, 491 (1999) 103; CPL, 296 (1998) 8; JACS, 118 (1996) 7689; J. Comp. Chem., 14 (1993) 895; Theochem 86 (1992) 315 Another matter: if you are interested in materials related to microelectronics and in case you missed it, please, check the web site of our Nano & Giga forum in Krakow at http://asdn.net/ngcm2004/ We have modeling and software design sections at the meeting. The deadline for abstracts submission is April 15th. Best regards, Anatoli Korkin ======== ANSWERS: ======== If you are interested in a careful comparison of experimental data with results generated by a wide range of methods and basis sets, I encourage you to use the superb NIST Website on benchmarks. The URL is http://srdata.nist.gov/cccbdb/ Wayne E. Steinmetz Coordinator of Molecular Biology Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz{at}pomona.edu WWW: pages.pomona.edu/~wsteinmetz --------------- Hi Anatoli, The following recent paper compares the accuracy of various semiempirical methods with DFT of over 1,000 compounds. Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation, James J. P. Stewart, J Mol Model (2004) 10:6-12 Regards, David Gallagher ---------- Dr. Korkin - I've done some comparisons and evaluations of methodologies for describing strong hydrogen-bonded complexes. The first reference cited below is an extensive comparison of various DFT approaches with ab initio methodologies up to MP2/6-311++G(d,p). The second reference is a review that covers ab initio, DFT, and semiempirical approaches. This is less detailed but covers more conceptual ground. The references are as follows: A. T. Pudzianowski, "A Sytematic Appraisal of Density Functional Methodologies for Hydrogen Bonding in Binary Ionic Complexes," J. Phys. Chem. 100(12), 4781-4789 (1996); A. T. Pudzianowski, "Current computational approaches to the strong hydrogen bond," Recent Res. Devel. in Physical Chem. 1, 81-97 (1997). I have reprints of both. Andrew Pudzianowski ------------- Dear Anatoli, there is a recent paper of J.J.P. Stewart: "Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation" J.Mol.Model. 2004, 10(1), 6-12. Regards, Anselm Horn ----------- I'm sorry; I've forgotten to attach the article: J. Phys. Chem A, 2003, 107, 11445 (K. Houk et al) Albena BULGARIA SHUMEN, 9700 UNIVERSITY OF SHUMEN DEPARTMENT OF NATURAL SCIENCES a.patleeva{at}shu-bg.net -------------------------- Calculations of electric properties, of molecules and clusters, are a good test for the performance of DFT functionals. Hope these three will be of help. Regards, D X AK: DX = Demetrios Xenides. Copies of papers received: J. Chem. Phys, 115 (2001) 7957 J. Phys. Chem. A (in press) Phys. Chem. Chem. Phys. 5 (2003) 1992 ------------ Dear colleague, I would advice to take a look at the chapter 8 (pages 233-273) "Density Functional Theory" in "Essentials of Computational Chemistry "by C.J. Cramer, Wiley, 2002 where this is discussed. Best regards, Patrick Senet -------------- Hi Anatoli, ... Thomas (Strassner) PS: Concerning your question: I do know that Ken Houk has prepared a manuscript where he tested several methods. Why don't you email him ? PPS: For teaching it would be a help to have such a list. Could you please send me a summary? ==================================== __________________________________ Do you Yahoo!? Yahoo! Small Business $15K Web Design Giveaway http://promotions.yahoo.com/design_giveaway/ From chemistry-request@ccl.net Thu Apr 8 14:56:53 2004 Received: from front3.chartermi.net (front3.chartermi.net [24.213.60.109]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i38JuqjR031704 for ; Thu, 8 Apr 2004 14:56:52 -0500 Received: from [24.236.135.230] (HELO mmserver) by front3.chartermi.net (CommuniGate Pro SMTP 4.0.6) with SMTP id 638216933 for chemistry.-at-.ccl.net; Thu, 08 Apr 2004 15:57:02 -0400 Message-ID: <000801c41da3$a5997970$0901a8c0@mmserver> From: "Jim Kress" To: References: Subject: DFT functionals comparison Date: Thu, 8 Apr 2004 15:56:56 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 I searched the CCL archive and could find nothing on this topic. Does anyone on the list know of (and would share) a (recent) comprehensive review of DFT functionals and the quality of their prediction of molecular properties? Thanks. Jim From chemistry-request@ccl.net Thu Apr 8 14:54:40 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i38JsejR031612 for ; Thu, 8 Apr 2004 14:54:40 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 57FAB48727 for ; Thu, 8 Apr 2004 15:54:11 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 13634-10 for ; Thu, 8 Apr 2004 15:54:03 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com (srvkyem1.americas.sc-world.com [10.16.100.68]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 1361B4880B for ; Thu, 8 Apr 2004 15:54:03 -0400 (EDT) X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C41DA3.3DD53B5C" Subject: help G98W atomic charges Date: Thu, 8 Apr 2004 15:54:02 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0047FD29.-at-.srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: help G98W atomic charges Thread-Index: AcQdoz3pNPX/fM63SbKPpANUQ50tFg== From: "Shobe, David" To: "CCL computational chemistry list (E-mail)" This is a multi-part message in MIME format. ------_=_NextPart_001_01C41DA3.3DD53B5C Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable 1. If you calculate CHELPG or MK charges (these are based on the = electric field generated by the molecule) with "heavy heavy" atoms, I = get an error message that there is no atomic radius (stored in the = program) for Ge (for example). I notice that there are keywords readradii and readatradii. But I don't = know what radius to input. Will just any tabulated "atomic radius" do? = 2. I would like to calculate GAPT charges also (these are based on how = the dipole moment changes as atoms are moved). But I can't find the = proper option under either pop or freq. How does one do a GAPT = calculation? If Gaussian can't do it is there another program that = reads the output or checkpoint file and does the calculation? --David Shobe ------_=_NextPart_001_01C41DA3.3DD53B5C Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable help G98W atomic charges

1. If you calculate CHELPG or MK = charges (these are based on the electric field generated by the = molecule) with "heavy heavy" atoms, I get an error message = that there is no atomic radius (stored in the program) for Ge (for = example).

I notice that there are keywords = readradii and readatradii. But I don't know what radius = to input. Will just any tabulated "atomic radius" = do?

2. I would like to calculate GAPT = charges also (these are based on how the dipole moment changes as atoms = are moved). But I can't find the proper option under = either pop or freq. How = does one do a GAPT calculation? If Gaussian can't do it is there = another program that reads the output or checkpoint file and does the = calculation?

--David Shobe

------_=_NextPart_001_01C41DA3.3DD53B5C-- From chemistry-request@ccl.net Thu Apr 8 14:04:55 2004 Received: from neptune.tranzymepharma.com (neptune.med.usherbrooke.ca [132.210.158.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i38J4sjR029969 for ; Thu, 8 Apr 2004 14:04:55 -0500 Received: from mercure.neokimia.com (exchange.tranzymepharma.com [192.168.1.3]) by neptune.tranzymepharma.com (8.12.10/8.12.10) with ESMTP id i38J51Qg015130 for ; Thu, 8 Apr 2004 15:05:01 -0400 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C41D9C.623C463C" Subject: FW: calculate accessible surface area for an occluded cavity X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Date: Thu, 8 Apr 2004 15:04:57 -0400 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: calculate accessible surface area for an occluded cavity thread-index: AcQdMh00qKO+dTeHTw2qV9K32Yp29QAaJ5iAAABocoA= From: "Axel Mathieu" To: "CCL" X-NK-Spam-Status: Ce message n'est pas du SPAM, (Score: 2.787, Requis: 5, FVGT_u_HAS_2LETTERFLDR,HTML_70_80,HTML_MESSAGE,J_CHICKENPOX_39,OACYS_SINGLE,RM_rb_ANCHOR,RM_rb_BREAK,RM_rb_DIV,RM_rb_FONT) X-NK-Spam-Version: SpamAssassin version 2.63 X-Scanned-By: MIMEDefang 2.42 This is a multi-part message in MIME format. ------_=_NextPart_001_01C41D9C.623C463C Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Qin, =20 Take a look at the freeware STC (Structure-based thermodynamic = calculations - these are based on SAS) developped by the PENCE/CIHR = group in Canada http://www.pence.ca/software/stc/html-4.3/stc.html. I = used STC to propose a cholesterol transfer mechanism for the StAR = protein (it conatins a cavity!). In case you're interested, my you'll = find my paper abstract and reference at: = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3DRetrieve = = &db=3Dpubmed&dopt=3DAbstract&list_uids=3D12459035 =20 STC can quickly report the SAS for each heavy atom of a residue and you = just have to add them up, or fill the cavity with the ligand and = calculate the difference (supposing your ligand fills the cavity) ... =20 APM =20 =20 -----Original Message----- From: Q [mailto:qzou.-at-.iupui.edu]=20 Sent: 7 avril, 2004 20:30 To: chemistry.-at-.ccl.net Subject: CCL:calculate accessible surface area for an occluded cavity =20 Dear All, I have a protein with an internal cavity that has no access to the = outside solvent. I would like to calculate the accessible surface area = of the residues inside the cavity to see how accessible they are to the = cavity. How can I do this or what programs could help to do it? How = about NACCESS? Thanks for any input. =20 Qin =20 ------_=_NextPart_001_01C41D9C.623C463C Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Qin,

Take a look at the freeware STC (Structure-based thermodynamic calculations = -=A0 these are based on SAS) developped = by the PENCE/CIHR group in Canada http://www.pe= nce.ca/software/stc/html-4.3/stc.html. I used STC to propose a cholesterol transfer mechanism for the StAR = protein (it conatins a cavity!). In case you’re interested, my you’ll = find my paper abstract and reference at: http://www.ncbi= .nlm.nih.gov/entrez/query.fcgi?cmd=3DRetrieve&db=3Dpubmed&dopt=3D= Abstract&list_uids=3D12459035

STC can quickly report the SAS for each heavy atom of a residue and you just = have to add them up, or fill the cavity with the ligand and calculate the = difference (supposing your ligand fills the cavity) = …

APM

-----Original = Message-----
From: Q = [mailto:qzou.-at-.iupui.edu]
Sent: 7 avril, 2004 20:30
To: chemistry.-at-.ccl.net
Subject: = CCL:calculate = accessible surface area for an occluded cavity

Dear = All,

I have a protein with = an internal cavity that has no access to the outside solvent. I would like = to calculate the accessible surface area of the residues inside the cavity = to see how accessible they are to the cavity. How can I do this or what = programs could help to do it? How about NACCESS? Thanks for any = input.

Qin

------_=_NextPart_001_01C41D9C.623C463C-- From chemistry-request@ccl.net Thu Apr 8 19:46:04 2004 Received: from chem.ucsb.edu (ultra.chem.ucsb.edu [128.111.114.119]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i390k3jR011376 for ; Thu, 8 Apr 2004 19:46:04 -0500 Received: from localhost (bushnell@localhost) by chem.ucsb.edu (8.11.7p1+Sun/8.11.7) with ESMTP id i390kA926147; Thu, 8 Apr 2004 17:46:10 -0700 (PDT) Date: Thu, 8 Apr 2004 17:46:10 -0700 (PDT) From: John Bushnell To: "Makowski, Mike" cc: chemistry.-at-.ccl.net Subject: Re: CCL:Enforcing symmetry within G98 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, The symmetry of your input structure is retained by default in g98. If g98 is "defaulting to C1 symmetry" your structure is probably not really C3 according to the cutoffs that Gaussian uses to detect symmetry. This can sometimes be overcome by constructing a Z-matrix with the correct symmetry, but this can become tricky depending on the structure. There may be an IOP option to loosen these cutoffs? It is obviously difficult to write an exactly symmetric structure with a C3 symmetry axis using cartesians with a finite number of digits... - John On Thu, 8 Apr 2004, Makowski, Mike wrote: > I am performing some geometry optimizations in vacuuo on some large > organo-metallic complexes with C3 or higher symmetry. > > My problem is that I cannot find a way to enforce this symmetry during > the optimization routine. Is there a set of keywords that can be > employed to prevent G98 from defaulting to C1 symmetry or to enforce a > particular symmetry? > > The structures we get using C1 optimizations are "reasonable", but > clearly should be much better. Based on the resultant bond lengths and > angles the symmetry is certainly not obeyed. > > Any help would be appreciated. > > -Mike > > Michael P. Makowski, Ph.D. From chemistry-request@ccl.net Thu Apr 8 19:57:32 2004 Received: from chem.ucsb.edu (ultra.chem.ucsb.edu [128.111.114.119]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i390vVjR011912 for ; Thu, 8 Apr 2004 19:57:31 -0500 Received: from localhost (bushnell@localhost) by chem.ucsb.edu (8.11.7p1+Sun/8.11.7) with ESMTP id i390vJK26409; Thu, 8 Apr 2004 17:57:19 -0700 (PDT) Date: Thu, 8 Apr 2004 17:57:19 -0700 (PDT) From: John Bushnell To: Vasile Chis cc: chemistry{at}ccl.net Subject: Re: CCL:specifying the connectivity in Gaussian In-Reply-To: <5.0.0.25.2.20040408091543.02280f98{at}phys.ubbcluj.ro> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, If there is no barrier between the Zwitterion and the neutral structure, then there is really no physically meaningful way to do a full geometry optimization while maintaining the Zwitterion if the neutral structure is lower in energy. However, there could be a local minimum that is Zwitterionic which is higher in energy which you might find with some careful surface scanning (which means that there is a barrier to forming the neutral form). - John On Thu, 8 Apr 2004, Vasile Chis wrote: > Dear Colleagues, > > I am trying to optimize a molecule (with Gaussian) with two charged groups, > +NH3 and COO-, respectively. However, during the optimization, one of the > amino hydrogen leaves the nitrogen and bound to one of the oxygen atoms of > COO group. > In order to preserve the two groups I imposed the same bond length for the > three NH bonds, but this means a restriction which even if does not led to > imaginary frequencies, however the corresponding optimized geometry must be > higher in energy than that in which an NH...O hydrogen bond is allowed. > The Help of the program says that there is a way of giving a specific > connectivity for atoms, however I was not able to solve my problem. I will > appreciate very much any help on this topic. > > Best regards and Happy Easter for everybody! > Vasile > > > ------------------------------------------- > Dr. Vasile Chis From chemistry-request@ccl.net Thu Apr 8 18:14:40 2004 Received: from smtp2.Stanford.EDU (smtp2.Stanford.EDU [171.67.16.116]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i38NEejR007489 for ; Thu, 8 Apr 2004 18:14:40 -0500 Received: from alphahelix (alphahelix.Stanford.EDU [171.64.126.26]) by smtp2.Stanford.EDU (8.12.11/8.12.11) with ESMTP id i38NEnIb024153; Thu, 8 Apr 2004 16:14:49 -0700 Reply-To: From: "Joseph Han" To: "'Jim Kress'" Cc: Subject: RE: DFT functionals comparison Date: Thu, 8 Apr 2004 16:15:00 -0700 Message-ID: <00da01c41dbf$517de260$1a7e40ab@alphahelix> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4024 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal In-Reply-To: <000801c41da3$a5997970$0901a8c0@mmserver> Jim, This might help: Tests of second-generation and third-generation density functionals for thermochemical kinetics Zhao, Y; Pu, JZ; Lynch, BJ; Truhlar, DG Source: PHYSICAL CHEMISTRY CHEMICAL PHYSICS; 2004; v.6, no.4, p.673-676 It covers barrier heights and atomization energies. They did leave out KMLYP however. We've run the same tests as described in the paper using KMLYP with the following results. BH6 AE6 MSE MUE MSE MUE KMLYP/DIDZ w/ HLC -2.86 2.86 -0.79 0.98 KMLYP/MG3S w/ HLC -2.92 2.92 0.18 0.45 KMLYP/6-311+G(2df,2p) w/ HLC -2.92 2.92 0.06 0.50 MMUE KMLYP w/ HLC 1.80 These results would place KMLYP near the top compared with all the other tested methods. The only method that does a better job predicting barrier heights is MPW1K, but the MPW1K atomization energies have a larger error. The KMLYP atomization energies are comparable with the best shown in the paper. Finally, the MMUE would be the best of all the methods evaluated. It is important to apply the high level correction (HLC) as specified in the original KMLYP reference in order to obtain good AE results. Hope this helps. Joseph Han Department of Chemical Engineering Stanford University 650-723-0420 FAX: 650-725-7294 > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request^at^ccl.net] On Behalf Of Jim Kress > Sent: Thursday, April 08, 2004 12:57 PM > To: chemistry^at^ccl.net > Subject: CCL:DFT functionals comparison > > > I searched the CCL archive and could find nothing on this topic. > > Does anyone on the list know of (and would share) a (recent) > comprehensive > review of DFT functionals and the quality of their prediction > of molecular > properties? > > Thanks. > > Jim > > > > > -= This is automatically added to each message by the mailing > script =- > To send e-mail to subscribers of CCL put the string CCL: on > your Subject: line > and send your message to: CHEMISTRY^at^ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST^at^ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the > maintainer: > Jan Labanowski, jlabanow^at^nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > >