From chemistry-request@server.ccl.net Fri Sep 13 02:36:24 2002 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8D6aN330907 for ; Fri, 13 Sep 2002 02:36:23 -0400 Received: from resu1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id IAA17428; Fri, 13 Sep 2002 08:34:04 +0200 (MEST) for chemistry@ccl.net Date: Fri, 13 Sep 2002 08:34:04 +0200 (MEST) Message-Id: <200209130634.IAA17428@resu1.ulb.ac.be> From: Pierre Mignon To: chemistry@ccl.net Subject: vizualizing amber output, summary. X-Mailer: Webmail ULB v2.1 Hello > From the answers for my question concerning free sofware for vizualizing amber outputs : VMD has been in majority cited. Thank you for all your answers. Pierre. Mignon Pierre PhD student Free University of Brussel (VUB) Dienst Algemene Chemie (ALGC) Pleinlaan, 2 1050 Brussels Belgium Tel + 32 2 629 35 16 Fax + 32 2 629 33 17 e-mail pmignon@vub.ac.be From chemistry-request@server.ccl.net Fri Sep 13 02:50:04 2002 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8D6o4331182 for ; Fri, 13 Sep 2002 02:50:04 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.12.6/8.12.6/Guy-23-01-2002) with ESMTP id g8D6o0rZ027546 for ; Fri, 13 Sep 2002 08:50:01 +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 IAA16022 for ; Fri, 13 Sep 2002 08:49:10 +0200 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3D81897B.EC33BAAA@lctn.uhp-nancy.fr> Date: Fri, 13 Sep 2002 08:45:15 +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: CCL Subject: Summary Lowdin atomic charges Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-milter arcturus (http://amavis.org/) Howdy, special thanks to Chris Cramer and Masao Masamura for the references concerning Lowdin atomic charges. Masao Masamura: tokin@mx3.tiki.ne.jp Please see Lowdin, P.-O. 1970. Adv. Quantum Chem., 5, 185. Also, please see Cusachts, L. C. and Politzer, P. 1968. Chem. Phys.Lett.,1, 529. Chris Cramer: cramer@pollux.chem.umn.edu 5 Loewdin, P.-O. J. Chem. Phys. 1950, 18, 365. 6 Golebiewski, A.; Rzescowska, E. Acta Phys. Pol. 1974, 45, 563. 7 Baker, J. Theor. Chim. Acta 1985, 68, 221. 8 Kar, T.; Sannigrahi, A. B.; Mukherjee, D. C. THEOCHEM 1987, 153, 93. Yours. -- ...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 Sep 13 13:56:37 2002 Received: from lulu.it.northwestern.edu ([129.105.16.54]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8DHub312778 for ; Fri, 13 Sep 2002 13:56:37 -0400 Received: (from mailnull@localhost) by lulu.it.northwestern.edu (8.12.3/8.12.3) id g8DHubxc029131 for ; Fri, 13 Sep 2002 12:56:37 -0500 (CDT) Received: from dwnwv01.northwestern.edu (pine-34-009204.nuts.northwestern.edu [129.105.9.204]) by lulu.it.northwestern.edu via smap (V2.0) id xma028702; Fri, 13 Sep 02 12:56:25 -0500 Message-Id: <5.1.0.14.2.20020913123611.00a917c0@lulu.it.northwestern.edu> X-Sender: cli099@lulu.it.northwestern.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 13 Sep 2002 12:56:22 -0500 To: chemistry@ccl.net From: Chunhui Li Subject: linear code to 2D or 3D structure Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi, if I only have bond connectivity information without coordinates for many molecules, is there any software I can use to get the 2D or 3D structure without drawing? thanks Chunhui c-li@northwestern.edu From chemistry-request@server.ccl.net Fri Sep 13 11:19:52 2002 Received: from quantix.u-strasbg.fr ([130.79.34.133]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8DFJq309401 for ; Fri, 13 Sep 2002 11:19:52 -0400 Received: from quantix.u-strasbg.fr (quantonakessa [130.79.34.222]) by quantix.u-strasbg.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id RAA63318 for ; Fri, 13 Sep 2002 17:20:10 +0200 Sender: saue@quantix.u-strasbg.fr Message-ID: <3D82020C.823B311B@quantix.u-strasbg.fr> Date: Fri, 13 Sep 2002 17:19:40 +0200 From: Trond SAUE X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.18-6mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: 2D chart of theoretical models Content-Type: multipart/alternative; boundary="------------3C71CE0355868981D0F0355C" --------------3C71CE0355868981D0F0355C Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit The quality of a calculation can be judged according to the choice of method and basis set and this is often depicted as a 2D chart. Pople is often associated with the origin of this chart and indeed such a chart is depicted in figure 1.1 of the book "Ab Initio Molecular Orbital Theory" by Hehre, Radom, Schleyer and Pople (1986). There is even a paper by Pople in JCP 43(1965) S229 entitled "Two-Dimensional Chart of Quantum Chemistry". However, this chart concerns the "hyperbola of quantum chemistry" with one axis given by sophistication (method and basis) and the other by the size of the system in terms of the number of electrons. Inbetween these dates the 2D method-basis chart has been alluded to by authors including Taylor, Schaefer and Dunning. Do anybody know more about the origins of the 2D chart of theoretical models ? Best regards, Trond Saue -- Trond SAUE (DIRAC: http://dirac.chem.sdu.dk/) Laboratoire de Chimie Quantique et Modélisation Moléculaire Université Louis Pasteur ; 4, rue Blaise Pascal ; F-67000 STRASBOURG tél: 03 90 24 13 01 fax: 03 90 24 15 89 email: saue@quantix.u-strasbg.fr --------------3C71CE0355868981D0F0355C Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit The quality of a calculation can be judged according to the choice of method and basis set
and this is often depicted as a 2D chart. Pople is often associated with the origin of this chart
and indeed such a chart is depicted in figure 1.1 of the book "Ab Initio Molecular Orbital
Theory" by Hehre, Radom, Schleyer and Pople (1986). There is even a paper by Pople in JCP 43(1965) S229
entitled "Two-Dimensional Chart of Quantum Chemistry". However, this chart concerns the "hyperbola
of quantum chemistry" with one axis given by sophistication (method and basis) and the other
by the size of the system in terms of the number of electrons. Inbetween these dates the
2D method-basis chart has been alluded to by authors including Taylor, Schaefer and Dunning.
Do anybody know more about the origins of the 2D chart of theoretical models ?
    Best regards,
       Trond Saue 
-- 
Trond SAUE                                (DIRAC: http://dirac.chem.sdu.dk/)
Laboratoire de Chimie Quantique et Modélisation Moléculaire
Université Louis Pasteur ; 4, rue Blaise Pascal ; F-67000 STRASBOURG
tél: 03 90 24 13 01   fax: 03 90 24 15 89   email: saue@quantix.u-strasbg.fr
  --------------3C71CE0355868981D0F0355C-- From chemistry-request@server.ccl.net Fri Sep 13 12:03:56 2002 Received: from pasteur ([164.2.255.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8DG3t310476 for ; Fri, 13 Sep 2002 12:03:56 -0400 Received: from lrb.ap-hop-paris.fr (localhost [127.0.0.1]) by pasteur.ap-hop-paris.fr (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H2D0052QWME0J@pasteur.ap-hop-paris.fr> for chemistry@ccl.net; Fri, 13 Sep 2002 18:03:50 +0200 (MEST) Date: Fri, 13 Sep 2002 17:07:39 -0700 From: Pong Subject: Need for Pharmacophore generation program Sender: pong@ap-hop-paris.fr To: chemistry@ccl.net Message-id: <3D827DCB.4FC84046@lrb.ap-hop-paris.fr> Organization: Service de Biochimie et de biologie moleculaire MIME-version: 1.0 X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: en Dear all, My name is Jaturong, I'm a student in faculty of pharmacy, Mahidol University, Thailand. Now I'm training in molecular modeling in France, for one year. My work now is concerning about the pharmacophore generation of ligands test set. I'm the beginner in this field. Now I've already constructed all of my ligands and use the molecular dynamic to find many conformers of each molecule. The next step, I need to superimpose and to locate the pharmacophoric point. I have ever know that there are commercial program to find the pharmacophore automatically. However, at this moment I cannot buy nothing, due to my crisis budget. So, I want to know that, is there any program to generation pharmacophore, free of charge for academic user or not? If you have any information about it, could you please to inform me. It's very important, because it is the critical objective of my work now. I will wait for your kindness, to help me. Sincerely yours, Jaturong From chemistry-request@server.ccl.net Fri Sep 13 23:17:41 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8E3He301786 for ; Fri, 13 Sep 2002 23:17:40 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id XAA91764 for ; Fri, 13 Sep 2002 23:05:59 -0400 (EDT) Date: Fri, 13 Sep 2002 23:05:59 -0400 From: Rick Venable To: chemistry@ccl.net Subject: CHARMM chloroform In-Reply-To: <5.1.0.14.2.20020913123611.00a917c0@lulu.it.northwestern.edu> Message-ID: ReplyTo: Rick_Venable@nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone have CHARMM parameters for chloroform that give reasonable density, and maybe dielectric constant? =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=