From chemistry-request@server.ccl.net Mon Apr 28 04:37:09 2003 Received: from hkusua.hku.hk ([147.8.2.91]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3S8b8o16536 for ; Mon, 28 Apr 2003 04:37:08 -0400 Received: from hkusua.hku.hk (localhost [127.0.0.1]) by hkusua.hku.hk (8.12.8p1/8.12.8/check_local5.4) with ESMTP id h3S81i38011481 for ; Mon, 28 Apr 2003 16:01:44 +0800 (HKT) X-Spam-Filter: check_local@hkusua.hku.hk by digitalanswers.org Received: from localhost (h9807907@localhost) by hkusua.hku.hk (8.12.8p1/8.12.8/Submit) with ESMTP id h3S81hPi011358 for ; Mon, 28 Apr 2003 16:01:44 +0800 (HKT) Date: Mon, 28 Apr 2003 16:01:43 +0800 (HKT) From: Wong Lai Ho X-Sender: h9807907@hkusua To: CHEMISTRY@ccl.net Subject: Gaussian Products Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-MailScanner: 0 Dear cclers, As it is well known that the product of two contracted gaussian function is a linear combination of gaussian primitives along the line joining the two centres of contracted gaussian functions. Is that possible to approximate the gaussians primitives distributed along the line by ONE gaussian primitive(or other form of function) centred on the line. Thanks in advance. Larry From chemistry-request@server.ccl.net Mon Apr 28 09:08:12 2003 Received: from Lilly.com ([40.33.1.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3SD8Co13953 for ; Mon, 28 Apr 2003 09:08:12 -0400 Received: from LILLY.COM ([40.59.1.39]) by INET.D48.LILLY.COM (PMDF V6.1-1 #30673) with ESMTP id <01KV95FA9NUU002TH5@INET.D48.LILLY.COM> for CHEMISTRY@ccl.net; Mon, 28 Apr 2003 08:08:12 -0500 (EST) Received: from mcntusmail28.d51.lilly.com (mcntusmail28.d51.lilly.com [40.1.134.45]) by NEWMAN.D52.LILLY.COM (PMDF V6.1-1 #30673) with ESMTP id <01KV95EXEW86000AQC@NEWMAN.D52.LILLY.COM> for CHEMISTRY@ccl.net; Mon, 28 Apr 2003 08:08:11 -0500 (EST) Content-return: prohibited Date: Mon, 28 Apr 2003 08:07:57 -0500 From: DURST_GREGORY@Lilly.com Subject: Re: CCL:xyz->zmat->xyz To: CHEMISTRY@ccl.net Message-id: MIME-version: 1.0 X-Mailer: Lotus Notes Release 5.07a May 14, 2001 Content-type: multipart/alternative; boundary="=_alternative 0048242B05256D16_=" X-MIMETrack: Serialize by Router on USMAIL28/AM/LLY(Release 5.0.10 |March 22, 2002) at 04/28/2003 08:08:10 AM, Serialize complete at 04/28/2003 08:08:10 AM This is a multipart message in MIME format. --=_alternative 0048242B05256D16_= Content-Type: text/plain; charset="us-ascii" Matt, As I recall from previous discussions on this topic, (see the CCL archives) there are very few programs that will do this, however, you can use MOPAC (most any version) to do a single point energy calc on your XYZ coordinates and you will get the Z-matrix in the output. Kludgy, but it works. The caveat is that you need to take care in building up your molecules. Always add new atoms to existing atoms to get proper torsions. For some structures you may have to re-number atoms to get what you want. Good luck! regards, Greg ---------------- Greg Durst Computational chemistry Eli Lilly & Co. Indianapolis, IN USA Matt Challacombe Sent by: Computational Chemistry List 04/27/2003 06:07 PM To: CHEMISTRY@ccl.net cc: Subject: CCL:xyz->zmat->xyz Hi, Is there a simple program for converting from xyz to z-matrix and back? I've spent quite a while examining different versions of babel, but none of them seem to work in this capacity... Thx, Matt -- Matt Challacombe Theoretical Division, Los Alamos http://www.t12.lanl.gov/~mchalla/ -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net --=_alternative 0048242B05256D16_= Content-Type: text/html; charset="us-ascii"
Matt,
As I recall from previous discussions on this topic, (see the CCL archives) there are very few programs that will do this, however, you can use MOPAC (most any version) to do a single point energy calc on your XYZ coordinates and you will get the Z-matrix in the output. Kludgy, but it works. The caveat is that you need to take care in building up your molecules. Always add new atoms to existing atoms to get proper torsions. For some structures you may have to re-number atoms to get what you want. Good luck!
regards,
Greg

----------------
Greg Durst
Computational chemistry
Eli Lilly & Co.
Indianapolis, IN  USA


Matt Challacombe <MChalla@lanl.gov>
Sent by: Computational Chemistry List <chemistry-request@ccl.net>

04/27/2003 06:07 PM

       
        To:        CHEMISTRY@ccl.net
        cc:        
        Subject:        CCL:xyz->zmat->xyz



Hi,

Is there a simple program for converting from xyz to
z-matrix and back?  I've spent quite a while examining
different versions of babel, but none of them seem to
work in this capacity...

Thx, Matt

--
Matt Challacombe      
Theoretical Division, Los Alamos          
http://www.t12.lanl.gov/~mchalla/



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--=_alternative 0048242B05256D16_=-- From chemistry-request@server.ccl.net Mon Apr 28 02:39:49 2003 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3S6dmo22276 for ; Mon, 28 Apr 2003 02:39:49 -0400 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Mon, 28 Apr 2003 08:39:15 +0200 Message-ID: <005d01c30d51$391cd9d0$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: "Matt Challacombe" , References: <200304271707.14141.MChalla@LANL.Gov> Subject: Re: CCL:xyz->zmat->xyz Date: Mon, 28 Apr 2003 08:41:39 +0200 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 5.50.4920.2300 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 Try Mol2mol, it has many Z-matrix option http://web.interware.hu/frenzy/mol2mol regards Tamas Dr. Tamas E. Gunda Department of Pharmaceutical Chemistry Medical and Health Center University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- From: "Matt Challacombe" To: Sent: Monday, April 28, 2003 01:07 Subject: CCL:xyz->zmat->xyz > Hi, > > Is there a simple program for converting from xyz to > z-matrix and back? I've spent quite a while examining > different versions of babel, but none of them seem to > work in this capacity... > > Thx, Matt > > -- > Matt Challacombe > Theoretical Division, Los Alamos > http://www.t12.lanl.gov/~mchalla/ > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Mon Apr 28 01:32:14 2003 Received: from [195.229.145.2] ([195.229.145.2]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3S5WCo15308 for ; Mon, 28 Apr 2003 01:32:13 -0400 Received: from no.name.available by [195.229.145.2] via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; Mon, 28 Apr 2003 09:19:20 +0400 Received: from FSD1G1D (gwd1b1h.zu.ac.ae [10.10.0.23]) by macsmtp.zu.ac.ae (8.12.5/8.12.5) with ESMTP id h3S5IT5k017981 for ; Mon, 28 Apr 2003 09:18:30 +0400 Received: from EMBADOMAIN-MTA by FSD1G1D with Novell_GroupWise; Mon, 28 Apr 2003 09:30:19 +0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0 Date: Mon, 28 Apr 2003 09:30:11 +0400 From: "Iman Boukhobza" To: , Subject: Re: CCL:xyz->zmat->xyz Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h3S5WGo15315 Hi Vega, winMopac can do the job Iman >>> Matt Challacombe 04/28/03 03:07AM >>> Hi, Is there a simple program for converting from xyz to z-matrix and back? I've spent quite a while examining different versions of babel, but none of them seem to work in this capacity... Thx, Matt -- Matt Challacombe Theoretical Division, Los Alamos http://www.t12.lanl.gov/~mchalla/ -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Mon Apr 28 09:21:47 2003 Received: from ultra3000.if.sc.usp.br ([143.107.228.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3SDLko15915 for ; Mon, 28 Apr 2003 09:21:46 -0400 Received: from joselap (zappa.if.sc.usp.br [143.107.228.35]) by ultra3000.if.sc.usp.br (8.11.6/8.11.0) with ESMTP id h3SDJ1318813 for ; Mon, 28 Apr 2003 10:19:01 -0300 Message-ID: <007001c30d89$44893830$0201a8c0@joselap> From: "JOSE" To: References: <65924360-776A-11D7-9FBB-000393B63452@wag.caltech.edu> Subject: Re: CCL:Slater basis sets Date: Mon, 28 Apr 2003 10:22:50 -0300 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 The program package called ADF - http://www.scm.com/ you see in the manual at page 17: "ADF employs Slater-type exponential basis functions centered on the atoms. Such a function consists of an exponential part exp(-ar) and a polynomial pre-factor rkrxkxykyzkz. A function set is characterized by its radial behavior (the exponential part and the power of r, kr) and by its angular momentum quantum number l. The functions in such a set consist of all possible combinations xkxykyzkx, such that kx+kx+kz=l. These are denoted the Cartesian spherical harmonics." as an option to this kind of basis, you may prefer to use Gaussian basis-set fitted to more sophisticated Slate-Type function contraction, like Double Zeta or Triple Zeta Slater functions. The choice depends on the availability and the system you are going to study. Subject: CCL:Slater basis sets > I'm doing some QMC calculations in which I would like to use Slater > (rather than Gaussian) basis sets. Can anyone recommend a good > reference for STO basis sets of different quality? I have the STO basis > sets that were used for the STO-NG (which can be found in Hehre, > Stewart, Pople JCP 51,2657 (1969), and Hehre, Ditchfield, Stewart, > Pople JCP 52, 2769 (1970)), but I don't have any others. Can any of the > CCLers out there point me to a good place to look? Thanks in advance. > > Rick > > Rick Muller > rpm@wag.caltech.edu > http://wag.caltech.edu/home/rpm > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Mon Apr 28 09:36:24 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3SDaOo17789 for ; Mon, 28 Apr 2003 09:36:24 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h3SDaPt05644; Mon, 28 Apr 2003 09:36:25 -0400 (EDT) Date: Mon, 28 Apr 2003 09:36:23 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: cartesians to z-mat and back Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I love MOLDEN and use it often for my geometry conversions. It comes with the Z-matrix editor: http://www.cmbi.kun.nl/~schaft/molden/molden.html It should be stressed that conversion of cartesians to Z-matrix can only be a trivial task for molecules that are trees (i.e., do not contain cycles). When rings (or more complicated arrangements, like cages, say, cubane) are present, the well behaved Z-matrix should contain dummy atoms. You can try to understand the problem by build the Z-matrix in such a way that changing one parameter does not affect any other parameters. For example, the z-matrix for benzene ring has to involve a centroid (a dummy atom in the center of the ring) or otherwise, changing one torsion angles within the ring will change other torsion angles. With the centroid, and the rays going from it to the real atoms, you can build a Z-matrix which does not involve dependencies between parameters. Now... Can the software detect such situations automatically and deal with them. Sure... However, quite frankly, I did not see much of such packages around. It is not a trivial problem, and even for simple molecules with cycles, there are many ways to represent their geometry as a Z-matrix. And deciding which Z-matrix is better, is again not a trivial thing. While there are obviously objective measures, this is still an art, and the beauty of the Z-matrix is in the eye of the beholder. And while there are methods which make Z-matrix less important for unconstrained optimization of the whole molecule (e.g., redundant internal coordinates in Gaussian), there is nothing better than a well behaved Z-matrix when doing partial optimizations of chosen geometrical features of the molecule(s), e.g., when studying transition states and reaction paths. Jan Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | E-mail: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/~jkl Columbus, OH 43212-1163 | http://www.ccl.net/ http://asdn.net/