From chemistry-request@server.ccl.net Fri May 24 03:28:35 2002 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4O7SZ123333 for ; Fri, 24 May 2002 03:28:35 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.12.3/8.12.3/Guy-23-01-2002) with ESMTP id g4O7SVxI025472; Fri, 24 May 2002 09:28:32 +0200 (METDST) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id JAA23434; Fri, 24 May 2002 09:26:57 +0200 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3CEDEB93.56A56DE9@lctn.uhp-nancy.fr> Date: Fri, 24 May 2002 09:28:19 +0200 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: Cameron Banks CC: chemistry@ccl.net Subject: Re: CCL:Valence Shell Electron Pair Repulsion theory References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-milter arcturus (http://amavis.org/) Hello, do you know this URL: http://neon.chem.ox.uk/vrchemistry/labintro/newdefault.html they have a very nice VSEPR tutorial and practical. If I remember correctly, it is a Java code. Even if you are not interested in web pages, you could try to ask for the code. They also have a very interesting symmetry practical. Hope this helps. -- ...Xav WARNING ! NEW PHONE AND FAX NUMBER !! Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 68 43 74 Universite Henri Poincare (F) 33 3 83 68 43 71 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Fri May 24 07:08:11 2002 Received: from spule.compch.tu-freiberg.de ([139.20.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4OB8B100605 for ; Fri, 24 May 2002 07:08:11 -0400 Received: from chemie.tu-freiberg.de (pc113.aoch.tu-freiberg.de [139.20.35.35]) by spule.compch.tu-freiberg.de (8.11.2/8.11.2/SuSE Linux 8.11.1-0.5) with ESMTP id g4OBB6U02979 for ; Fri, 24 May 2002 13:11:14 +0200 Message-ID: <3CEE1FB5.7050402@chemie.tu-freiberg.de> Date: Fri, 24 May 2002 13:10:45 +0200 From: Uwe Boehme User-Agent: Mozilla/5.0 (Windows; U; Win98; de-DE; rv:0.9.4) Gecko/20011019 Netscape6/6.2 X-Accept-Language: de-DE MIME-Version: 1.0 To: chemistry@ccl.net Subject: Problem: GIAO calculation of ferrocenyl compound Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCL'ers I encountered a problem in calculation of NMR chemical shift of a ferrocenyl compound: First I have optimized the geometry of the molecule and calculated the Hessian matrix. Second I made a single point calculation with HF method and the basis set 6-311+G(2d,p). Then I wanted to calculate the NMR-shift.(see example below) ------------------------------------------------------- %NProc=4 %Mem=2GB %Chk=fc05d.chk # HF/6-311+G(2d,p) SP Test # iop(6/7=3) gfinput scfcyc=900 Ferrocenyl-(SiMe2)6-Ph, NMR HF/6-311+G(2d,p) 0 1 Fe -0.202906 0.111404 7.470024 H 0.083021 0.820915 10.194050 C -0.654386 0.704438 9.410643 C -1.354170 -0.497869 9.090560 H -0.700081 2.731516 8.453903 ....etc. coordinates of the molecule --Link1-- %NProc=4 %Mem=2GB %Chk=fc05d.chk # HF/6-311+G(2d,p) NMR Geom=AllCheck Guess=Read Test scfcyc=900 Ferrocenyl-(SiMe2)6-Ph, NMR HF/6-311+G(2d,p) 0 1 ------------------------------------------------------- The calculated NMR-shift for iron is nonsense. Shifts of atoms connected directly to iron are also wrong. Atoms which are further away have shift values which make sense. (see examples below) ------------------------------------------------------- Inverted reduced A of dimension 34 with in-core refinement. Calculating GIAO nuclear magnetic shielding tensors. SCF GIAO Magnetic shielding tensor (ppm): 1 Fe Isotropic =*********** Anisotropy =399287.5804 XX=*********** YX=*********** ZX= 93002.8604 XY=*********** YY=*********** ZY=*********** XZ= 94358.4550 YZ=*********** ZZ=*********** Eigenvalues:********************** 1669.3510 2 H Isotropic = 63.4665 Anisotropy = 241.8958 XX= -140.7531 YX= 88.9387 ZX= -99.0583 XY= -131.3972 YY= 165.3069 ZY= 36.0108 XZ= 21.4654 YZ= 72.3870 ZZ= 165.8456 Eigenvalues: -146.2706 111.9397 224.7303 3 C Isotropic = 695.5235 Anisotropy = 785.0543 XX= 121.6982 YX= 699.4741 ZX= -566.8338 XY= -59.0868 YY= 1081.0732 ZY= 97.1838 XZ= -54.6052 YZ= 293.6058 ZZ= 883.7992 Eigenvalues: -103.2821 970.9596 1218.8931 ....etc. 30 Si Isotropic = 422.8279 Anisotropy = 32.8879 XX= 397.0723 YX= 13.0645 ZX= 3.0779 XY= 2.9391 YY= 435.9510 ZY= 8.5848 XZ= 9.8744 YZ= 5.0853 ZZ= 435.4603 Eigenvalues: 394.8440 428.8865 444.7531 31 C Isotropic = 204.6798 Anisotropy = 19.0621 XX= 192.2924 YX= 11.0580 ZX= -8.3426 XY= -7.4119 YY= 216.0632 ZY= 1.2366 XZ= 0.1573 YZ= 6.6130 ZZ= 205.6837 Eigenvalues: 190.8175 205.8340 217.3879 32 H Isotropic = 45.1076 Anisotropy = 16.0320 XX= 38.4798 YX= 16.9477 ZX= -16.3021 XY= -4.0497 YY= 48.1692 ZY= 0.3816 XZ= -5.8285 YZ= 6.8300 ZZ= 48.6737 Eigenvalues: 28.6116 50.9155 55.7956 ------------------------------------------------------- What is wrong here? I hope anybody can help me to solve this problem! Sincerely Yours Uwe Boehme. Sender: _______________________________________________________ Dr. Uwe Boehme Institut fuer Anorganische Chemie Technische Universitaet Bergakademie Freiberg 09596 Freiberg Germany e-mail: uwe.boehme@chemie.tu-freiberg.de http://www.uweboehme.de _______________________________________________________ From chemistry-request@server.ccl.net Fri May 24 07:05:56 2002 Received: from mail-b.bcc.ac.uk ([144.82.100.22]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4OB5u100518 for ; Fri, 24 May 2002 07:05:56 -0400 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Fri, 24 May 2002 12:05:54 +0100 Received: (from uccatvm@localhost) by socrates-a.ucl.ac.uk (8.11.6+Sun/8.9.3) id g4OB5rY19857 for chemistry@ccl.net; Fri, 24 May 2002 12:05:53 +0100 (BST) From: uccatvm Message-Id: <200205241105.g4OB5rY19857@socrates-a.ucl.ac.uk> Subject: Re: CCL:BSSE To: chemistry@ccl.net (CCL) Date: Fri, 24 May 2002 12:05:53 +0100 (BST) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Olegas, > In the "standard" BSSE equation (for a dimer AB): > > BSSE(AB) =3D E(AB)^AB - E(A)^A - E(B)^B + [E(A')^A - E(A')^AB + E(B)^B - = > E(B)^AB] > > I've got most of the parameters, but how in G98W do I calculate E(A)^AB = > and E(B)^AB, i.e. the energy of the monomer units in terms of the dimer = > basis set. With Gaussian, the keyword Massage has to be used for counterpoise corrections (assuming it's the same for G98 and G98W). Have a look at the Gaussian manual: http://www.gaussian.com/00000452.htm. There is an example there as well. However, don't believe the sentence about counterpoise being only a crude estimate, have a look at the following papers to learn more about BSSE and Counterpoise: - F.B. van Duijneveldt, J.G.C.M. van Duijneveldt-van de Rijdt, and J.H. van Lenthe, Chem. Rev. 94, 1873, 1994 (on counterpoise theory) - S. Simon, M. Duran, J.J. Dannenberg, J. Chem. Phys. 105, 1996 (on geometry optimizations on BSSE-corrected potential energy surfaces). - F.B. van Duijneveldt, "Basis Superposition Error" in "Molecular Interactions" S. Scheiner (ed.), Wiley (1997) - T. van Mourik, A.K. Wilson, K.A. Peterson, D.E. Woon, T.H. Dunning, Jr., Adv. Quant. Chem. 31, 105, 1999 (showing BSSE effects on interaction energies, distances, and frequencies). HTH, Tanja -- ===================================================================== Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik@ucl.ac.uk London WC1H 0AJ, UK home: tanja@netcomuk.co.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html ===================================================================== From chemistry-request@server.ccl.net Fri May 24 08:51:02 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4OCp1104349 for ; Fri, 24 May 2002 08:51:01 -0400 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id IAA23464; Fri, 24 May 2002 08:50:18 -0400 (EDT) Sender: richard@cornell.edu Message-ID: <3CEE370B.3FF5EE3C@cornell.edu> Date: Fri, 24 May 2002 08:50:19 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: "Pavel A. Petukhov" CC: chemistry@ccl.net Subject: Re: CCL:movie of docking References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Docking problems are small enough that you could possibly run a single trajectory and wait long enough to actually see a docking occur. This is after all how simulated annealing works. But you will waste a lot of time waiting for this to happen ... it will be a rare event. The easier thing to do is to run a trajectory in reverse starting in a docked configuration. Hamiltonian dynamics is time-reversible so the undocking trjectory is simply a docking trajectory with the signs of the momenta (or time) reversed. This trick has been used for years. Any number of simulation programs will probably work for this purpose. Richard Gillilan MacCHESS, Cornell From chemistry-request@server.ccl.net Fri May 24 10:52:05 2002 Received: from naex017w ([204.27.156.103]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4OEq5109142 for ; Fri, 24 May 2002 10:52:05 -0400 Received: from naex000b.apci.com ([144.249.178.60]) by 144.249.122.105 with Trend Micro InterScan Messaging Security Suite for SMTP v5.01; Fri, 24 May 2002 10:46:27 -0400 Received: by naex000b.apci.com with Internet Mail Service (5.5.2655.55) id ; Fri, 24 May 2002 08:50:06 -0400 Message-ID: From: "Peterson,Brian K." To: "'Xavier ASSFELD'" Cc: chemistry@ccl.net Subject: RE: Valence Shell Electron Pair Repulsion theory Date: Fri, 24 May 2002 08:50:03 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: text/plain; charset="iso-8859-1" I think you mean: http://neon.chem.ox.ac.uk/vrchemistry/vsepr/intro/vsepr_splash.html -----Original Message----- From: Xavier ASSFELD [mailto:Xavier.Assfeld@lctn.uhp-nancy.fr] Sent: Friday, May 24, 2002 3:28 AM To: Cameron Banks Cc: chemistry@ccl.net Subject: CCL:Valence Shell Electron Pair Repulsion theory Hello, do you know this URL: http://neon.chem.ox.uk/vrchemistry/labintro/newdefault.html they have a very nice VSEPR tutorial and practical. If I remember correctly, it is a Java code. Even if you are not interested in web pages, you could try to ask for the code. They also have a very interesting symmetry practical. Hope this helps. -- ...Xav WARNING ! NEW PHONE AND FAX NUMBER !! Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 68 43 74 Universite Henri Poincare (F) 33 3 83 68 43 71 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Fri May 24 09:01:32 2002 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4OD1W104913 for ; Fri, 24 May 2002 09:01:32 -0400 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id QAA06550; Fri, 24 May 2002 16:00:10 +0300 (EET DST) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Fri, 24 May 2002 16:00:10 +0300 (EET DST) From: Mikael Johansson X-Sender: To: Uwe Boehme cc: Subject: Re: CCL:Problem: GIAO calculation of ferrocenyl compound In-Reply-To: <3CEE1FB5.7050402@chemie.tu-freiberg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-15 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g4OD1W104914 Hello Uwe and All! On Fri, 24 May 2002, Uwe Boehme wrote: > Second I made a single point calculation with HF method > and the basis set 6-311+G(2d,p). [...] > The calculated NMR-shift for iron is nonsense. I don't believe HF is a good choice for calculating NMR shifts, or much else, for transition metals. Personally I have no experience on this matter though, so maybe someone on the list has other comments? Try using DFT, you might have better luck. See for example: M. Bühl, "Density functional computations of transition metal NMR chemical shifts: dramatic effects of Hartree-Fock exchange", Chem. Phys. Lett. 267 (1997) 251-257 Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson@helsinki.fi http://www.helsinki.fi/~mpjohans/ Phone: +358-9-191 50185 FAX : +358-9-191 50169 From chemistry-request@server.ccl.net Fri May 24 10:22:36 2002 Received: from jacobus.chem.smu.edu ([129.119.201.27]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4OEMZ107985 for ; Fri, 24 May 2002 10:22:35 -0400 Received: from localhost (zmz@localhost) by jacobus.chem.smu.edu (8.11.6/8.11.6) with ESMTP id g4OEFDA15538; Fri, 24 May 2002 09:15:13 -0500 Date: Fri, 24 May 2002 09:15:13 -0500 (CDT) From: Pearl Zheng To: cc: Ibrahim Moustafa Subject: Summary of Re: CCL:FlexX help needed In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="2004949961-1595422502-1022249713=:14435" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. --2004949961-1595422502-1022249713=:14435 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Ibrahim and CCL users, I got some answers for the FlexX Formal Charges problem. I attached the answers for you. And my experiment carried out that we can set the flag of Assign_Formal_Charges to 0 (automatically assignment OFF) or 1(automatically assignment ON) through the Graphic User Interface panel of Sybyl FlexX. Then we can assign formal charges manually in the ligand.mol2 file when flag is 0. Thanks for everyone's kindly help. -----Mingzhu Southern Methodist University On Wed, 22 May 2002, Ibrahim Moustafa wrote: > Hello Pearl, > > I'm interested in your question. Can you forward me the answers you'll > get? > > Thanks, > Ibrahim > > Name :Ibrahim M.Moustafa > Mail address :Center for Biomolecular Science, > BIOMOLECULAR SCIENCE BUILDING, > North Haugh,St-Andrews, > Fife,KY16 9ST > Scotland,U.K. > Tel :+44(0)1334-467257 > E-mail :im17@st-andrews.ac.uk > > On Tue, 21 May 2002, Pearl Zheng wrote: > > > Hi dear CCL users, > > > > I am using sybyl FlexX to docking a small molecule to the active site of > > an enzyme. But the assignment of formal charges automatically by FlexX > > only works well in simple case. My question is how can I assign formal > > charge by myself. The second question is can I use Gasteiger-Huckel > > charges while doing FlexX? > > > > All response are appreciated. > > > > ---Mingzhu > > > > > > > > > > -= This is automatically added to each message by mailing script =- > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > > > > > > > --2004949961-1595422502-1022249713=:14435 Content-Type: TEXT/PLAIN; charset=en_GB; name=flexxhelp Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: Formal Charges in FlexX Content-Disposition: attachment; filename=flexxhelp RnJvbSBqbGVAd29ybGQuc3RkLmNvbSBUaHUgTWF5IDIzIDE3OjUxOjM0IDIw MDINCkRhdGU6IFdlZCwgMjIgTWF5IDIwMDIgMDY6Mzk6MTEgLTA0MDAgKEVE VCkNCkZyb206IEpvZSBNIExlb25hcmQgPGpsZUB3b3JsZC5zdGQuY29tPg0K 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chemistry-request@server.ccl.net Fri May 24 14:20:41 2002 Received: from mr.usu.edu ([129.123.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4OIKf116310 for ; Fri, 24 May 2002 14:20:41 -0400 Received: from pc3 (pc3.chem.usu.edu [129.123.3.37]) by mr.usu.edu (Postfix) with SMTP id 825361D3E1 for ; Fri, 24 May 2002 12:20:41 -0600 (MDT) Reply-To: From: "Tapas Kar" To: Subject: Semiempirical programs on IR/Raman spectra Date: Fri, 24 May 2002 12:18:34 -0600 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001E_01C2031D.1FBED450" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_001E_01C2031D.1FBED450 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Dear CClers, Could any one tell me if there are free softwares available for doing IR, Raman, XPS, NMR etc spectra using MNDO/PM3/AM1 theories. Tapas *********************************************** "We owe a lot to the Indians, who taught us how to count, without which no worthwhile scientific discovery could have been made." - Albert Einstein - "The value of pi was first calculated by Budhayana, and he explained the concept of what is now known as the Pythagorean Theorem. British scholars have last year (1999) officially published that Budhayan’s works dates to the 6th Century, which is long before the European mathematicians." ---------------------------------------------------------------------------- ---- Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar@cc.usu.edu Web:http://www.chem.usu.edu/faculty/Tapas/index.html ------=_NextPart_000_001E_01C2031D.1FBED450 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear CClers,

 Could any one tell me if = there are=20 free softwares available for doing

 IR,=20 Raman, XPS, NMR etc spectra using MNDO/PM3/AM1 = theories.

Tapas

***********************************************
"We owe a lot to the Indians, who taught = us how to=20 count, without
which no worthwhile scientific discovery could have = been=20 made."
         &n= bsp;           &nb= sp;           &nbs= p;        =20 - Albert Einstein -
"The value = of pi was=20 first calculated by Budhayana, and he explained
the concept of what = is now=20 known as the Pythagorean Theorem. British
scholars have last year = (1999)=20 officially published that Budhayan=92s
works dates to the 6th = Century, which is=20 long before the=20 European
mathematicians."
----------------------------------= ----------------------------------------------
Tapas=20 Kar, Ph. D
Department of Chemistry & Biochemistry
Utah State=20 University
Logan, UT 84322-0300

Tel: 435-797-7230
Fax:=20 435-797-3390
Email: tapaskar@cc.usu.edu
Web:http://www.chem.usu.edu/faculty/Tapas/index.html

 
------=_NextPart_000_001E_01C2031D.1FBED450-- From chemistry-request@server.ccl.net Fri May 24 08:13:35 2002 Received: from math.fu-berlin.de ([160.45.40.10]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4OCDZ102879 for ; Fri, 24 May 2002 08:13:35 -0400 Received: (qmail 19754 invoked by uid 9804); 24 May 2002 14:13:34 +0200 Received: from cognac.math.fu-berlin.de (160.45.41.44) by leibniz.math.fu-berlin.de with SMTP; 24 May 2002 14:13:31 +0200 Received: from localhost ([127.0.0.1] helo=math.fu-berlin.de ident=antony) by cognac.math.fu-berlin.de with esmtp (Exim 3.12 #1 (Debian)) id 17BDwp-0000dk-00 for ; Fri, 24 May 2002 14:13:31 +0200 Sender: antony@ccl.net Message-ID: <3CEE2E6B.3C6F4FB@math.fu-berlin.de> Date: Fri, 24 May 2002 14:13:31 +0200 From: Jens Antony X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.6 i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL post Subject: SUMMARY: Normal mode scan Content-Type: multipart/mixed; boundary="------------92E8770A4B29628241B5468D" X-Virus-Scanned: by AMaViS 0.3.12pre7 [19745] (NAI-uvscan@math.fu-berlin.de) X-Remote-IP: 160.45.41.44 This is a multi-part message in MIME format. --------------92E8770A4B29628241B5468D Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL, here are the answers to my request from last Friday. Thanks again. Jens Antony -- Free University Berlin Institute for Mathematics II Arnimallee 2-6 D-14195 Berlin , Germany --------------92E8770A4B29628241B5468D Content-Type: text/plain; charset=us-ascii; name="request" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="request" -- Request -- Dear CCL, 1) How can I scan a potential energy surface along a vibrational normal mode with Gaussian or another molecular electronic structure program automatically ? 2) How can I increase the precision of the normal modes printed with Gaussian ? --------------92E8770A4B29628241B5468D Content-Type: text/plain; charset=us-ascii; name="answer1" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="answer1" -- Answer 1 -- Hi Jens, you might try POLYRATE. It is a program (designed by Prof. Joel Bowman and others) to calculate vibrational frequencies and more by going beyond the harmonic oscillator approximation. Add the HPFREQ option to the FREQ command. You can find a very thorough documentation of G98 at: http://www.gaussian.com/techinfo.htm Stefan Fau --------------92E8770A4B29628241B5468D Content-Type: text/plain; charset=us-ascii; name="answer2" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="answer2" -- Answer 2 -- >1) How can I scan a potential energy surface along a vibrational normal I have a very crude fortran program that, when you give it the hpmodes output for a mode, will create a multi step g98 input file that scans (and computes what you want) along a mode. It is not automatic, and it is rather ugly, but it seems to work for me. I'd be happy to send you a copy if you'ld like. >2) How can I increase the precision of the normal modes printed with The hpmodes keyword will do this. Steve Williams --------------92E8770A4B29628241B5468D Content-Type: text/plain; charset=us-ascii; name="answer3" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="answer3" -- Answer 3 -- >1) How can I scan a potential energy surface along a vibrational normal G98 claims to be able to do this using freq as an option to IRC, alas that is not the case. The gaussian people says that it will work in rev. B. Please do let me know if you get an answer to this question. Theis Ivan Soelling --------------92E8770A4B29628241B5468D Content-Type: text/plain; charset=us-ascii; name="answer4" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="answer4" -- Answer 4 -- The FREQ=HPModes option will print out the normal modes to higher precision. Douglas J. Fox -- --------------92E8770A4B29628241B5468D-- From chemistry-request@server.ccl.net Fri May 24 21:16:10 2002 Received: from biosino.org ([202.127.18.238]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4P1G9107519 for ; Fri, 24 May 2002 21:16:10 -0400 Received: from mao [202.127.18.233] by biosino.org (SMTPD32-6.04) id A5E3D1301A0; Sat, 25 May 2002 09:16:19 +0800 Date: Sat, 25 May 2002 9:18:14 +0800 From: "xmao@biosino.org" To: "chemistry@ccl.net" Subject: MEP charge fitting using GAMESS-US? X-mailer: FoxMail 3.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <200205250916885.SM00279@mao> Dear everyone: Here is a question that I need some examples. I wonder if the molecular electrostatic potential based charge fitting could be done in GAMESS-US. If so, would you please give me some examples. Thanks. Regards, mao