From chemistry-request@server.ccl.net Thu Aug 2 09:53:19 2001 Received: from boeck.fmp-berlin.de ([194.95.129.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f72DrJ512056 for ; Thu, 2 Aug 2001 09:53:19 -0400 Received: from max.fmp-berlin.de (max.fmp-berlin.de [194.95.129.79]) by boeck.fmp-berlin.de (8.9.3/8.9.3/991227-Hbl) with SMTP id PAA02625 for <@boeck.fmp-berlin.de:chemistry@ccl.net>; Thu, 2 Aug 2001 15:52:23 +0200 (MEDT) Received: from fmp-berlin.de (localhost [127.0.0.1]) by max.fmp-berlin.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id PAA01544 for ; Thu, 2 Aug 2001 15:53:25 +0200 Sender: uwe@fmp-berlin.de Message-ID: <3B695B55.686A7E6F@fmp-berlin.de> Date: Thu, 02 Aug 2001 15:53:25 +0200 From: Uwe Richter X-Mailer: Mozilla 4.7 [en] (X11; U; IRIX64 6.4 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Program PERSCAN Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, does anybody know whether the program PERSCAN still exists on our planet, and if so, whether it is downloadable somewhere? I'd also appreciate suggestions about programs having similar capabilities. Thanks a lot. I will summarize, Uwe uwe@fmp-berlin.de From chemistry-request@server.ccl.net Thu Aug 2 08:32:17 2001 Received: from nenuphar.saclay.cea.fr ([132.166.192.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f72CWH509450 for ; Thu, 2 Aug 2001 08:32:17 -0400 Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.D20+Y2K) with ESMTP id OAA27716 for ; Thu, 2 Aug 2001 14:32:01 +0200 (MET DST) Received: from petunia.bruyeres.cea.fr (petunia.bruyeres.cea.fr [132.165.64.1]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.2.D20+Y2K) with ESMTP id OAA02071 for ; Thu, 2 Aug 2001 14:32:00 +0200 (MET DST) Received: from styx.bruyeres.cea.fr (styx-e76.bruyeres.cea.fr [132.165.76.3]) by petunia.bruyeres.cea.fr (8.9.3+Sun/jtpda-5.3.2) with ESMTP id OAA04060 for ; Thu, 2 Aug 2001 14:31:59 +0200 (MET DST) Received: by styx.bruyeres.cea.fr; id OAA21160; Thu, 2 Aug 2001 14:31:59 +0200 (MET DST) Message-Id: <200108021231.OAA21160@styx.bruyeres.cea.fr> Sender: Didier.MATHIEU@cea.fr Date: Thu, 02 Aug 2001 14:27:53 +0200 From: Didier MATHIEU X-Mailer: Mozilla 4.72 [fr] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: dipole moment derivatives Content-Type: multipart/alternative; boundary="------------C8678366FF8F13B561A6B8EE" --------------C8678366FF8F13B561A6B8EE Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I don't know how to obtain dipole moment derivatives from Gaussian94 calculations, preferably without calculation of the frequencies ? Regards -- Didier Mathieu CEA - Le Ripault BP 16 37260 Monts +33 02 47 34 41 85 --------------C8678366FF8F13B561A6B8EE Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hello,
I don't know how to obtain dipole moment derivatives from Gaussian94 calculations,
preferably without calculation of the frequencies ?
Regards 
-- 
Didier Mathieu
CEA - Le Ripault
BP 16
37260 Monts
+33 02 47 34 41 85
  --------------C8678366FF8F13B561A6B8EE-- From chemistry-request@server.ccl.net Thu Aug 2 12:22:34 2001 Received: from ozone.umsl.edu ([134.124.105.185]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f72GMY516350 for ; Thu, 2 Aug 2001 12:22:34 -0400 Received: from ozone.umsl.edu (localhost [127.0.0.1]) by ozone.umsl.edu (SGI-8.9.3/8.9.3) with ESMTP id LAA58107 for ; Thu, 2 Aug 2001 11:25:56 -0700 (PDT) Sender: siva@ozone.umsl.edu Message-ID: <3B699B33.EAA70B3C@ozone.umsl.edu> Date: Thu, 02 Aug 2001 11:25:55 -0700 From: Sivanesan Dakshanamurthy Organization: University of Missouri-St. Louis X-Mailer: Mozilla 4.51 [en] (X11; I; IRIX64 6.5 IP27) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: help Content-Type: multipart/alternative; boundary="------------D9817E9067D022E7B251C921" --------------D9817E9067D022E7B251C921 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCLers, Onceagain I'm asking for an help, about how and which forcefield could I use for my enzyme-substrate interactions. Please note that enzyme active site has a Zn cation. Thanks in advance, I would appreciate your help, Thanks, Sincerely, D.Sivanesan -- ( @ @ ) -------------------------------------------o00o----(_)----o00o---------------------- D. Sivanesan, Ph.D., Post Doctoral Fellow, Department of Chemistry, Computational Chemistry Group, University of Missouri, St. Louis, Missouri-63121. USA Phone: 314-516-6882 (Office) 314-389-4777 (Home) sivanesan15@hotmail.com and chedsiva@jinx.umsl.edu Fax : 314-516-5342 ------------------------------------------------------------------------------------ --------------D9817E9067D022E7B251C921 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCLers,
Onceagain I'm asking for an help, about how and which forcefield could I use for my enzyme-substrate interactions. Please note that enzyme active site has a Zn cation.
Thanks in advance,
I would appreciate your help,
Thanks,
Sincerely,
D.Sivanesan 
-- 
                                                 ( @ @ )
-------------------------------------------o00o----(_)----o00o----------------------
D. Sivanesan, Ph.D.,                       
Post Doctoral Fellow,            
Department of Chemistry,               
Computational Chemistry Group,       
University of Missouri,                             
St. Louis, Missouri-63121. USA                      
Phone: 314-516-6882 (Office)                         
       314-389-4777 (Home)                         
       sivanesan15@hotmail.com and  chedsiva@jinx.umsl.edu                        
Fax : 314-516-5342                                     
------------------------------------------------------------------------------------
  --------------D9817E9067D022E7B251C921-- From chemistry-request@server.ccl.net Thu Aug 2 17:38:53 2001 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f72Lcr501286 for ; Thu, 2 Aug 2001 17:38:53 -0400 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id f72LcmH12005 for ; Thu, 2 Aug 2001 16:38:49 -0500 (CDT) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.9.3+Sun/8.9.1) with ESMTP id QAA09282 for ; Thu, 2 Aug 2001 16:38:48 -0500 (CDT) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Thu, 2 Aug 2001 16:38:48 -0500 (CDT) From: Jim Phillips To: chemistry@ccl.net Subject: NAMD 2.3 Release Announcement Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII +--------------------------------------------------------------------+ | | | NAMD 2.3 Release Announcement | | | +--------------------------------------------------------------------+ August 2, 2001 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.3 has several advantages over NAMD 2.2: - AMBER file compatibility (parm and coordinate input only). - The new psfgen tool for building PSF structure files. - Simpler to run on a single workstation. (No more rsh!) - New ports to the Compaq AlphaServer SC, Scyld Beowulf, and Mac OS X. - Improved serial performance, particularly with PME on Alpha. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. For your convenience, NAMD has been ported to and will be installed on both the PSC TCS1 Alpha cluster and the NCSA Platinum Linux cluster. Please consider the performance advantages of running NAMD when you apply for time on these new resources. Benchmarks for your proposal are available at http://www.ks.uiuc.edu/Research/namd/performance.html The Theoretical Biophysics Group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From chemistry-request@server.ccl.net Thu Aug 2 19:06:25 2001 Received: from VAX.PHR.UTEXAS.EDU ([128.83.164.1]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f72N6P502768 for ; Thu, 2 Aug 2001 19:06:25 -0400 Received: by VAX.PHR.UTEXAS.EDU for chemistry@ccl.net; Thu, 2 Aug 2001 18:10:12 -0500 Date: Thu, 2 Aug 2001 18:10:12 -0500 From: PEARLMAN@VAX.PHR.UTEXAS.EDU To: chemistry@ccl.net Message-Id: <010802181012.5561@VAX.PHR.UTEXAS.EDU> Subject: Re: CCL:accessible atom or residues on protein surface Hello -- Regarding the issue of identifying atoms/residues on the solvent accessible surface of a protein, songm@rpi.edu (Minghu) wrote: > I had tried the several softwares to calculate the solvent accesible > area or relative %area of per atom or residue. But in order to pick > out those groups on the protein surface, I also have to define a > threthod value for the surface area. (for example, let is say, if > the surface area of one certain residue is larger than 30%, we can > assume the residue is on the protein surface.) So my question will > turn into : how large will this reasonable value roughly be? > ( from the view of biochemistry and chemistry) > > Of course I can try some arbitrary values, select out the assumed > suface group and finally check them by comparing with some > general-used softwares.But since I just began my work, so I am very > interested in know whether any previous works/references about this > question or are there any other methods instead of calculating > solvent accesible areas. Dr. Felix Deanda (a former grad student, now at GlaxoSmithKline/RTP) and I have recently submitted a manuscript on this subject and I would be glad to provide pre-prints. Meanwhile, here are a few very brief comments in response to Minghu's inquiry: > are there any other methods instead of calculating > solvent accesible areas. We reviewed the literature and tested five methods for identifying the surface atoms of macromolecules. The method based on calculating atomic contributions to the surface area was, *by far*, the best. We also demonstrated that using efficient software for the surface area (or solvent accessible surface area) calculation yields results in very acceptable cpu times (less than 10 seconds on a modest PC). > I had tried the several softwares to calculate the solvent accesible > area or relative %area of per atom or residue. Most applications requiring (or benefitting from) a specification of the "protein surface" would be best served by a list of "surface atoms" as opposed to a list of "surface residues". > But in order to pick > out those groups on the protein surface, I also have to define a > threthod value for the surface area. > ... > how large will this reasonable value roughly be? > ( from the view of biochemistry and chemistry) We explicitly addressed the issue of a threshold surface area value for distinguishing "surface atoms" from "interior atoms". Clearly, any atom with non-zero surface area is a "true surface atom." The issue boils down to asking "How much of the true surface am I willing to ignore?" Using a-chymotrypsin (6CHA) as an example: threshold (A^2): 0.010 0.025 0.250 1.000 2.500 % total Area: 100.000 99.998 99.902 99.266 97.430 % total atoms: 53.16 52.65 48.15 41.37 34.64 Averaged over six proteins of diverse size and shape (6CHA, 1RA2, 3FXN, 7TLN, 1TIM, 3TRA), our recommended threshold value of 1.0 A^2 yields 99.16% of the true surface areas. > how large will this reasonable value roughly be? > ( from the view of biochemistry and chemistry) If one were developing some sort of surface-based model of some protein-related property, weighting the contributions of "surface atoms" according to their actual surface areas seems to be the best way to address what Minghu probably had in mind when he added "from the view of biochemistry and chemistry". I hope my comments have been helpful. -- Bob Robert S. Pearlman, Ph.D Coulter R. Sublett Regents Chair in Pharmacy and Director, Laboratory for the Development of Computer-Assisted Drug Discovery Software College of Pharmacy University of Texas Austin, Texas 78712 512-471-3383 (voice) 512-471-7474 (FAX) pearlman@naphthyl.phr.utexas.edu From chemistry-request@server.ccl.net Thu Aug 2 18:02:34 2001 Received: from spot-us.spotfire.com ([63.118.157.70]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f72M2X501730 for ; Thu, 2 Aug 2001 18:02:34 -0400 Received: from shawn (spot-us.spotfire.com [172.16.1.10]) by spot-us.spotfire.com (Postfix) with SMTP id 36A437F4CF for ; Thu, 2 Aug 2001 18:02:28 -0400 (EDT) From: "Shawn Kenner X1522" To: Subject: Symposium Announcement: Linking Genomic Information with Drug Design Date: Thu, 2 Aug 2001 18:03:50 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f72M2Y501731 The Computers in Chemistry Division of the ACS (COMP), along with CINF and MEDI, are pleased to announce an exciting symposium to be held at the Chicago ACS National Meeting, August 26-30, 2001. This symposium, Linking Genomic Information with Drug Design, will bring together experts from bioinformatics, structural biology, medicinal chemistry, cheminformatics, molecular biology and more to discuss the latest trends and findings at the interface of these dynamic fields. The symposium, organized by Jim Arnold of Structural GenomiX, will feature speakers from both academia and industry for coverage of emerging methods and practical applications. Join us for this symposium and an evening reception where you can meet with colleagues and speakers. For more information and the full symposium schedule please see http://membership.acs.org/C/COMP/seminar.html. We look forward to seeing you there! (Note: CINF is the ACS Division of Chemical Information, and MEDI is the ACS Division of Medicinal Chemistry.) Shawn Kenner PR Chair, COMP Shawn Kenner Director, Cheminformatics Spotfire, Inc. 212 Elm. Street Somerville, MA 02144 shawn@spotfire.com