From owner-chemistry@ccl.net Thu May 4 10:57:00 2006 From: "Paul Fleurat-Lessard Paul.Fleurat-Lessard/./ens-lyon.fr" To: CCL Subject: CCL:G: Cartesian Coordinate Transformation Message-Id: <-31685-060504060332-15777-+lF2LP0yYsqgWnez8hTc8Q]^[server.ccl.net> X-Original-From: Paul Fleurat-Lessard Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 04 May 2006 11:12:51 +0200 MIME-Version: 1.0 Sent to CCL by: Paul Fleurat-Lessard [Paul.Fleurat-Lessard(a)ens-lyon.fr] Hi, >> I am using Gaussian to optimized geometries with constraints and my input format is in cartesian coordinate. But after optimization, somtimes, Gaussian output does not contain my original cartesian coordinate information. Instead, it reports "standard orientation", which is a transformation of my original coordinate. I am just wondering if there is an easy way or tools to transform Gaussian "starndard orientation" back to my cartesian coordinate. As already mentionned, you can play with the iniertia tensor, but this can lead to orientation problem. I think that a more robust way is to use quaternion procedure as in the rmsd calculation. You can find details in: J Comput Chem 25: 1849 ­1857, 2004, 'Using Quaternions to Calculate RMSD' , EVANGELOS A. COUTSIAS, CHAOK SEOK, KEN A. DILL and download a f90 routine in: http://www.math.unm.edu/~vageli/homepage.html Regards, Paul. -- Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard=ens-lyon.fr Laboratoire de Chimie Ecole Normale Supérieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allée d'Italie Fax: + 33 (0)4 72 72 88 60 69364 Lyon Cedex 07 From owner-chemistry@ccl.net Thu May 4 12:39:00 2006 From: "DEJAEGERE Annick annick|*|titus.u-strasbg.fr" To: CCL Subject: CCL: =?WINDOWS-1252?Q?2006_ISQBP_President=92s_Meeting,_June_24-27,_S?= =?WINDOWS-1252?Q?trasbourg,_France?= Message-Id: <-31686-060504045404-6128-7PbityxVL4fMbF5HjJN2Ow,,server.ccl.net> X-Original-From: DEJAEGERE Annick Content-Type: multipart/alternative; boundary=Apple-Mail-8-919780913 Date: Thu, 4 May 2006 10:18:25 +0200 Mime-Version: 1.0 (Apple Message framework v749.3) Sent to CCL by: DEJAEGERE Annick [annick[a]titus.u-strasbg.fr] --Apple-Mail-8-919780913 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed 2006 ISQBP President=92s Meeting, June 24-27, Strasbourg, France Registration for the 2006 ISQPB President's Meeting in Strasbourg, =20 France on June 24-27 is on going. Meeting topics include Computer-Aided Drug Design/Molecular Recognition Large Scale Conformational Changes of Biomolecules Enzyme Catalysis via QM/MM methods Protein-Nucleic Acid Interactions Please access the meeting web site to register online as well as to =20 obtain additional information on the meeting http://isqbp.umaryland.edu/2006_meeting/ISQBP_presidents_2006.html Poster titles and abstracts are due upon registration. Email as WORD doc or rtf files to alex[-]outerbanks.umaryland.edu Please use 12 pt Arial font and limit the abstracts to one page. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D Dr. Annick P. Dejaegere Biocomputing group Structural Biology & Genomics Dept. - IGBMC - UMR7104 Ecole Sup=E9rieure de Biotechnologie de Strasbourg (ESBS) PARC INNOVATION - BOULEVARD SEBASTIEN BRANT BP 10413 - F-67412 ILLKIRCH - CEDEX Office: 33 3 90 24 47 21 FAX: 33 3 90 24 47 18 Email annick[-]igbmc.u-strasbg.fr --Apple-Mail-8-919780913 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=WINDOWS-1252
2006 ISQBP = President=92s Meeting, June 24-27, Strasbourg, France

on June 24-27 is on = going.

Meeting topics include

Large Scale Conformational Changes of = Biomolecules
Enzyme Catalysis via QM/MM = methods
Protein-Nucleic Acid = Interactions

Please access the meeting web site to register = online as well as to obtain
additional = information on the meeting

http://isqbp.umaryland.edu/2006_meeting/ISQBP_presidents_2006.html


Poster = titles and abstracts are due upon registration.
Email as WORD doc or rtf files to alex[-]outerbanks.umaryland.ed= u
Please use 12 pt Arial font and = limit the abstracts to one page.



=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Dr. Annick P. Dejaegere
Structural Biology & = Genomics Dept. - IGBMC - UMR7104

Ecole Sup=E9rieure de Biotechnologie de Strasbourg = (ESBS)
PARC INNOVATION - BOULEVARD = SEBASTIEN BRANT
BP = 10413 - F-67412 ILLKIRCH - CEDEX

Office:=A0=A033 3 90 24 47 21=A0=A0FAX:=A0=A033 3 90 24 47 18

= --Apple-Mail-8-919780913-- From owner-chemistry@ccl.net Thu May 4 16:11:00 2006 From: "Young Leh youngleh%gmail.com" To: CCL Subject: CCL: Molden Windows Version? Message-Id: <-31687-060504160948-18311-62q+mcOdTVhGie3Iq3WBzg#server.ccl.net> X-Original-From: "Young Leh" Date: Thu, 4 May 2006 16:09:41 -0400 Sent to CCL by: "Young Leh" [youngleh\a/gmail.com] Hi there, I downloaded Molden 4.1 for Windows here http://www.cmbi.ru.nl/molden/windowsnt95.html . But it looks to me Molden is not running on my computer. Does anybody have ever met the same problem and could point out how to solve this? thanks Young Leh From owner-chemistry@ccl.net Thu May 4 16:45:00 2006 From: "Dwayne Joseph dwayne_joseph!^!hotmail.com" To: CCL Subject: CCL:G: Regarding Gaussian Message-Id: <-31688-060503181107-4602-WeuvjBIBao9I3DhAA3qbAw[A]server.ccl.net> X-Original-From: "Dwayne Joseph" Content-Type: text/plain; format=flowed Date: Wed, 03 May 2006 21:23:55 +0000 Mime-Version: 1.0 Sent to CCL by: "Dwayne Joseph" [dwayne_joseph]~[hotmail.com] Hello, I am a physics graduate student and i have a question regarding GAUSSIAN98. Is it possible to extract the molecular orbitals (coeff) that are written to the IOPs when a Potential Energy Surface Scan (PES) is performed? And if so, how do i extract them? I have noticed that MO's are written for the initial structure and for the final structure, but not for the steps in between. Any help in resolving this matter will be greatly appreciated. Thank you -Dwayne Joseph
"... I believe in God because when it is my time to go I will go!"
- Ashraff from Pakistan
From owner-chemistry@ccl.net Thu May 4 17:21:01 2006 From: "Debasis Sengupta dxs++cfdrc.com" To: CCL Subject: CCL: Molden Windows Version? Message-Id: <-31689-060504163147-28655-eTV4VU/pEWHPZfJVxI97+A|,|server.ccl.net> X-Original-From: Debasis Sengupta Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 04 May 2006 15:33:41 -0500 MIME-Version: 1.0 Sent to CCL by: Debasis Sengupta [dxs],[cfdrc.com] You have to have X-window running at the background in order for molden to work. I use free X-window of cygwin. If you have, you can run Exceed in the passive mode before molden is started. What's the error you get? Young Leh youngleh%gmail.com wrote: >Sent to CCL by: "Young Leh" [youngleh\a/gmail.com] >Hi there, > >I downloaded Molden 4.1 for Windows here http://www.cmbi.ru.nl/molden/windowsnt95.html . > >But it looks to me Molden is not running on my computer. Does anybody have ever met the same problem and could point out how to solve this? > >thanks > >Young Leh> > > > > From owner-chemistry@ccl.net Thu May 4 18:36:01 2006 From: "Molsoft Training andy[A]molsoft.com" To: CCL Subject: CCL: Workshop: Modern Drug Target Crystallography and Structure Based Drug Discovery Message-Id: <-31690-060504163147-1234-IL2YnwvD7VMXRnKlS2CzCA**server.ccl.net> X-Original-From: Molsoft Training Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 04 May 2006 09:18:57 -0700 MIME-Version: 1.0 Sent to CCL by: Molsoft Training [andy : molsoft.com] We still have a few seats available for a two day workshop on the cutting-edge developments in crystallography and structure-based drug design. The workshop will be held on May 25-26, 2006 in La Jolla California. More info and registration form can be found here: http://ruppweb.dyndns.org/workshops/Molsoft_workshop.htm The workshop will be conducted jointly by: Dr. Bernhard Rupp (Founder qed life science discoveries, inc) and Prof. Ruben Abagyan (Professor of Molecular Biology at The Scripps Research Institute and Founder of Molsoft LLC). The workshop entitled "Modern Drug Target Crystallography and Structure Based Drug Design" (http://ruppweb.dyndns.org/workshops/Molsoft_workshop.htm) is suitable for executives, scientists, and technicians in the field of biological sciences and drug discovery, who wish to expand their knowledge in the rapidly advancing field of high throughput drug target crystallography and structure guided drug discovery. This workshop is designed for those who are considering using crystallography and virtual ligand screening as a tool in their drug discovery research and wish to get an overview of the techniques as well as researchers already familiar with crystallography and in-silico, analysis, modeling and docking, who wish to learn more about the latest developments in this field. For more information please visit: http://ruppweb.dyndns.org/workshops/Molsoft_workshop.htm E mail andy]=[molsoft.com or call (858 625 2000 x108). -- From owner-chemistry@ccl.net Thu May 4 21:17:00 2006 From: "Nuno A. G. Bandeira nuno.bandeira ~ ist.utl.pt" To: CCL Subject: CCL: Molden Windows Version? Message-Id: <-31691-060504174503-18634-Nf7/pSDarmhUDSuEnDy/OQ.:.server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 04 May 2006 22:05:05 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira#%#ist.utl.pt] Young Leh youngleh%gmail.com wrote: > Sent to CCL by: "Young Leh" [youngleh\a/gmail.com] > Hi there, > > I downloaded Molden 4.1 for Windows here http://www.cmbi.ru.nl/molden/windowsnt95.html . You must run molden from an X emulator like the one in cygwin. The batch file they provide is intended to run the starnet X emulator. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student ++ IST,Lisbon --