From chemistry-request@server.ccl.net Fri Dec 20 09:41:10 2002 Received: from gatekeeper.tripos.com ([192.160.145.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBKEf9i28791 for ; Fri, 20 Dec 2002 09:41:09 -0500 Received: (from uucp@localhost) by gatekeeper.tripos.com (8.11.6+Sun/8.11.6) id gBKEdpY19245 for ; Fri, 20 Dec 2002 08:39:51 -0600 (CST) Received: from cairo.tripos.com(172.20.176.21) by gatekeeper.tripos.com via csmap (V6.0) id srcAAAc4aGLL; Fri, 20 Dec 02 08:39:49 -0600 Received: (from nmalcolm@localhost) by cairo.tripos.com (SGI-8.9.3/8.9.3) id OAA50956; Fri, 20 Dec 2002 14:42:33 GMT Date: Fri, 20 Dec 2002 14:42:33 GMT Message-Id: <200212201442.OAA50956@cairo.tripos.com> X-Authentication-Warning: cairo.tripos.com: nmalcolm set sender to nmalcolm@tripos.com using -f From: "Nathaniel O.J. Malcolm" To: jos.lommerse@organon.com CC: chemistry@CCL.NET, marlous.vanvuuren@organon.com In-reply-to: <639D20177889D41198A600508BAD3CA1039AD2DD@capella3.oss.akzonobel.nl> (jos.lommerse@organon.com) Subject: Re: CCL:Constrained geometry optimisation with GAUSSIAN98 Sender: nmalcolm@tripos.com Reply-To: nmalcolm@tripos.com Organization: Tripos UK Ltd. References: <639D20177889D41198A600508BAD3CA1039AD2DD@capella3.oss.akzonobel.nl> Jos, If you want to do a proper constrained optimisation in Gaussian you are much better off using a Z-matrix and Opt=Z-Mat then setting the required dihedrals as constants. As far as I understand it the constraints withing the delocalised internal coordinates can only be applied in a approximate way due to the converstion between cartesian and the redundant internal coordinate sets. Noj -- -------------------------------- Dr. N.O.J. Malcolm Software Support Scientist Tripos UK Ltd nmalcolm@tripos.com Tel +44 (0)1908 650020 Fax +44 (0)1908 650001 -------------------------------- Sybyl, Unity and other products are exclusive property of Tripos & are protected trademarks, copyrights, & patents as appropriate The information in this e-mail is confidential and may have associated legal obligations. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender. From chemistry-request@server.ccl.net Fri Dec 20 11:17:53 2002 Received: from imaph.bas-net.by ([80.94.164.102]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBKGHli30461 for ; Fri, 20 Dec 2002 11:17:47 -0500 Received: from igor (igor [10.1.1.15]) by imaph.bas-net.by (8.12.5/8.12.5) with ESMTP id gBKFOK37015166 for ; Fri, 20 Dec 2002 17:24:20 +0200 Date: Fri, 20 Dec 2002 17:17:33 +0200 From: Igor Avilov X-Mailer: The Bat! (v1.45) Educational Reply-To: Igor Avilov X-Priority: 3 (Normal) Message-ID: <3098965925.20021220171733@imaph.bas-net.by> To: chemistry@ccl.net Subject: optimization in the excited state Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello! Could anybody help me with the following problem, please? I need to optimize the geometry of a molecule in the excited singlet state and to calculate its vibrational spectrum in this state. I know how to do it in Gaussian at CIS level. But i'd like to do it by Time dependent DFT because I did all others calculations by DFT. The second question I'm interested in is: is it possible to use the geometry which is connected with some vibrational mode. I mean: when the vibrational spectrum is calculated one can "animate" vibrations for example in HyperChem to visualize them. I'd like to use this geometry distorted by vibration. Thank you in advance, Merry Christmas, Igor Avilov. -- Best regards, Igor mailto:avilov@imaph.bas-net.by From chemistry-request@server.ccl.net Fri Dec 20 23:43:47 2002 Received: from net.bluemoon.net ([63.237.147.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBL4hli05296 for ; Fri, 20 Dec 2002 23:43:47 -0500 Received: from localhost (fantom@localhost) by net.bluemoon.net (8.12.4/8.12.4) with ESMTP id gBL4hir7092146; Fri, 20 Dec 2002 23:43:44 -0500 (EST) (mail-from fant@pobox.com) X-Authentication-Warning: net.bluemoon.net: fantom owned process doing -bs Date: Fri, 20 Dec 2002 23:43:44 -0500 (EST) From: Andrew Fant X-X-Sender: fantom@net.bluemoon.net To: jmmckel@attglobal.net cc: chemistry@ccl.net Subject: Re: CCL:Looking for a program to clean Fortran In-Reply-To: <3E03988B.9018D299@attglobal.net> Message-ID: <20021220233748.N91126-100000@net.bluemoon.net> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII John, I've always been partial to flow and floppy, two programs from CERN (oddly enough, written IN Fortran) that can be used to clean up dusty decks and do analysis of the code structure. FTNCHEK is another tool you might want to look at. It doesn't clean code in and of itself, IIRC, but it does a static analysis of the code and reports semantic errors and violations of good code practices. I've used these programs together to clean up old code myself (including MOPAC and AMPAC). Hope this helps, Andy Andrew Fant | This | "If I could walk THAT way... Molecular Geek | Space | I wouldn't need the talcum powder!" fant@pobox.com | For | G. Marx (apropos of Aerosmith) Boston, MA USA | Hire | http://www.pharmawulf.com On Fri, 20 Dec 2002 jmmckel@attglobal.net wrote: > CCLers, > > I have some Fortran code that desperately needs cleaning up. Is there > any free/inexpensive software available to do this? > > Thanks! > > John McKelvey > > > > -= 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 Fri Dec 20 13:18:57 2002 Received: from antivirus1.its.rochester.edu ([128.151.57.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBKIIui31922 for ; Fri, 20 Dec 2002 13:18:57 -0500 Received: from antivirus1.its.rochester.edu (localhost [127.0.0.1]) by antivirus1.its.rochester.edu (8.12.4/8.12.4) with ESMTP id gBKIIuLQ002045 for ; Fri, 20 Dec 2002 13:18:56 -0500 (EST) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus1.its.rochester.edu (8.12.4/8.12.4) with SMTP id gBKIIunf002042 for ; Fri, 20 Dec 2002 13:18:56 -0500 (EST) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.4/8.12.1) with ESMTP id gBKIIp8W009387 for ; Fri, 20 Dec 2002 13:18:51 -0500 (EST) Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz@mail.rochester.edu Organization: university of rochester To: chemistry@ccl.net Subject: help for NAMD Date: Fri, 20 Dec 2002 13:16:19 -0500 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200212201316.19267.weiz@mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gBKIIvi31923 Dear all: When I use NAMD to run the equilibration of a small system. it keep saying: "Warning: Not all atoms have unique coordinates." and "Warning: xxx margin violations detected during timestep xxx." but I checked the coordinates file and everything looks fine. could anybody tell me what is wrong? regards wei From chemistry-request@server.ccl.net Fri Dec 20 15:12:46 2002 Received: from haste.ibpc.fr ([193.49.235.208]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBKKCji01123 for ; Fri, 20 Dec 2002 15:12:45 -0500 Received: from lbl.gov (localhost.localdomain [127.0.0.1]) by haste.ibpc.fr (8.11.2/8.11.2) with ESMTP id gBKK8ZB02133; Fri, 20 Dec 2002 21:08:35 +0100 Message-ID: <3E0378C3.1040900@lbl.gov> Date: Fri, 20 Dec 2002 21:08:35 +0100 From: Edward Berry Reply-To: eaberry@lbl.gov User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: FyD CC: chemistry@ccl.net, pdb-l@sdsc.edu Subject: Re: pdb-l: Looking for a program_II References: <1040394290.3e032832e8f3a@webmail.u-picardie.fr> <3E0355DF.6070505@lbl.gov> <1040408323.3e035f03cfedb@webmail.u-picardie.fr> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit FyD wrote: > Dear Edward Berry, Dear All, > > >>How do you want to specify the 'modification of orientation' >>in a non-graphical program? If you can specify a rotation >>matrix or rotation angle about an axis defined >>by direction cosines, or a series of rotations about >>principal axes, then this is a very simple program. >>pdbset (CCP4) or moleman (USF) do this and much more, >>and are free to academic users. Otherwise they meet >>your criteria. > > > I get a lot of answers with graphical rotation controls using the mouse: I > think I have to explain how I "would like/need" to control the orientation of > my structure: I am NOT interested in controlling the orientation of my > structures using the mouse, i.e. I am NOT interested in a graphical control but > I would like to control the orientation using for instance atom names (in a > script): > - I would like first to put the center of mass at 0, 0, 0 > - Then, select 2 atom names "A", "B" to define the O -> x axis and a third > one, "C" to define the plane o, x, y. Then, apply the rotation as previously > defined and save the structure to 'a' format. Moleman will move the center of gravity to the origin, perform rotations (and translations) specified in a number of different ways, and write out the coordinates in pdb (or other) formats. If you need to also put an atom on the X axis, or a pair of atoms parallel to X to define a standard position before starting the rotations, you may need to do some programming to save the origin-shifted file, grep out the atoms involved, and do some algebra to determine the required rotation. But if you can just use the original orientation, centered, as your starting position then moleman will do everything. The manual is at: http://xray.bmc.uu.se/usf/moleman_man.html Look at the commands ORIGin_move and ROTAte_molecule > - I would also be interested in any other non-graphical reorientation > procedure. The idea is simply to have 'a' control of the structure orientation. Posibilities are a full rotation matrix, eulerian angles, or an axis and the rotation about it. I can't put my hands on a good reference for the conventions now- maybe a crystallography testbook. You can also use LSQman to calculate an operator to take certain atoms to the position of certain other atoms by rotation/translation. > > I also forgot to tell you that I need to load an input structure at a format > allowing at least 4 digits after the decimal points and obviously to save the > ouput reoriented structure with these same 4 digits. It means PDB format can be > used but the saved structure must be writen with these 4 digits. Another > solution are the sybyl or xyz formats. > > Thanks, regards, Francois > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l . From chemistry-request@server.ccl.net Fri Dec 20 13:03:49 2002 Received: from camdmail01.cam.accelrys.com ([192.190.183.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBKI3ni31719 for ; Fri, 20 Dec 2002 13:03:49 -0500 To: chemistry@ccl.net Subject: Accelrys Nanotechnology Modeling training workshop MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: gerhard@accelrys.com Date: Fri, 20 Dec 2002 18:03:43 +0000 X-MIMETrack: Serialize by Router on camdmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 12/20/2002 06:03:49 PM, Serialize complete at 12/20/2002 06:03:49 PM Content-Type: multipart/alternative; boundary="=_alternative 0063378880256C95_=" This is a multipart message in MIME format. --=_alternative 0063378880256C95_= Content-Type: text/plain; charset="us-ascii" Accelrys Inc. has joined with the organizers of the NanoTech 2003 conference and Prof Nick Quirke from Imperial College London to offer a one-day workshop in "Molecular Modeling of Nanomaterials" on February 28th in San Francisco, CA. The aim of this workshop is to introduce participants to current modeling methods and their use in predicting the properties of nanomaterials, The workshop will be based on the Materials Studio modeling environment, and consider methods reaching > from quantum mechanics, via classical atomistic to mesoscale. Following an introductory lecture by Prof. Nick Quirke, participants will carry out tutorials on dedicated PCs. The workshop will cover the following: - Introduction to Modeling of Nanomaterials. - Introduction to the Materials Studio modeling environment. - Nanotech modeling tutorials using quantum mechanics, classical, and mesoscale methods. Costs are $200 for commercial, $150 for government and $100 for academic. For course details and registration see: http://www.accelrys.com/training/matsci/schedule.html For Nanotech2003 conference details, see: http://www.nanotech2003.com/ Judith Madeley Accelrys Training Gerhard Goldbeck-Wood Accelrys Materials Science BU gerhard@accelrys.com Phone: +44 1223 228500 Fax: +44 1223 228501 http://www.accelrys.com --=_alternative 0063378880256C95_= Content-Type: text/html; charset="us-ascii"
Accelrys Inc. has joined with the organizers of the NanoTech 2003 conference
and Prof Nick Quirke from Imperial College London to offer a one-day workshop in
"Molecular Modeling of Nanomaterials" on February 28th in San Francisco, CA.

The aim of this workshop is to introduce participants to current modeling methods and
their use in predicting the properties of nanomaterials, The workshop will be based on
the Materials Studio modeling environment, and consider methods reaching from quantum
mechanics, via classical atomistic to mesoscale. Following an introductory lecture
by Prof. Nick Quirke, participants will carry out tutorials on dedicated PCs.

The workshop will cover the following:
- Introduction to Modeling of Nanomaterials.
- Introduction to the Materials Studio modeling environment.
- Nanotech modeling tutorials using quantum mechanics, classical, and mesoscale methods.

Costs are $200 for commercial, $150 for government and $100 for academic.

For course details and registration see:
http://www.accelrys.com/training/matsci/schedule.html

For Nanotech2003 conference details, see:
http://www.nanotech2003.com/
Judith Madeley
Accelrys Training

Gerhard Goldbeck-Wood
Accelrys Materials Science BU
gerhard@accelrys.com

Phone: +44 1223 228500
Fax:     +44 1223 228501
http://www.accelrys.com --=_alternative 0063378880256C95_=--