From chemistry-request@server.ccl.net Mon Mar 18 04:52:07 2002 Received: from pat.bath.ac.uk (IDENT:exim@[138.38.32.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2I9q7p29015 for ; Mon, 18 Mar 2002 04:52:07 -0500 Received: from mary.bath.ac.uk ([138.38.32.14] ident=mmdf) by pat.bath.ac.uk with smtp (Exim 3.12 #1) id 16mto5-0001ML-00; Mon, 18 Mar 2002 09:51:57 +0000 Received: from prpcn144 ( prpc-n144.bath.ac.uk [138.38.128.144] ) by mary.bath.ac.uk id aa29222 ; 18 Mar 2002 09:51 +0000 From: James Robinson To: "JEAN P. BLAUDEAU" Cc: Chemistry Subject: RE: No Subject Given By The Author Date: Mon, 18 Mar 2002 09:52:18 -0000 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g2I9q7p29016 Schrodinger do a pKa calc that is a QSAR using QM results. There was a good paper in J.Amer.Chem.Soc last year on ab initio calcs to predict pka. It's a difficult area as the slightest error will give erroneous results. Mr James J Robinson B.Sc. (HONS) MRSC M.Phil Molecular Modeller Pharmacy and Pharmacology Dept. University of Bath Claverton Down Bath, Somerset, UK. BA2 7AY. J.J.Robinson@bath.ac.uk http://www.bath.ac.uk tel +44(0) 1225 826826 ext 4723 -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of JEAN P. BLAUDEAU Sent: 15 March 2002 18:01 To: chemistry@ccl.net Subject: No Subject Given By The Author Hello, I am wondering if anyone would know of any programs that can calculate pKa's quantum mechanically. I think ChemCad calculates them semi-empirically, but I would prefer a QM method. Thank you, Jean --------------------------------------------------------------------------- Jean-Philippe Blaudeau ASC/HP, 2435 5th Street, Bldg. 676 Director of Computational Wright-Patterson Air Force Base Chemistry and Materials Ohio, 45433-7802 PET ASC MSRC & Phone: 937-904-5145 HPTi FAX: 937-255-4585 Email: blaudejp@asc.hpc.mil URL: http://www.asc.hpc.mil/PET/CCM --------------------------------------------------------------------------- -= 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 Mon Mar 18 03:50:25 2002 Received: from oc30.uni-paderborn.de ([131.234.240.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2I8oPp28108 for ; Mon, 18 Mar 2002 03:50:25 -0500 Received: (from ib@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) id MAA65142; Mon, 18 Mar 2002 12:26:56 +0100 (CET) Date: Mon, 18 Mar 2002 12:26:56 +0100 (CET) Message-Id: <200203181126.MAA65142@oc30.uni-paderborn.de> X-Authentication-Warning: oc30.uni-paderborn.de: ib set sender to ib@oc30.uni-paderborn.de using -f From: Ingo Brunberg To: r.e.oakes@btconnect.com CC: chemistry@ccl.net In-reply-to: Subject: Re: CCL:*.xyz files References: Check the MIME types of your webserver. Sounds like chemical/x-xyz is not registered correctly. Regards, Ingo > Dear CCL > > I have been trying to put some *.xyz on my web site. they are supposed to > show vibrational motion in molecules using the chime plugin. although pdb > files work perfectly ,there is always an error reported when I try to look > at the vibrations online. they work perfectly well on my local machine > though. I sent one of the file + the chime script to a friend to see if she > could get it to work via her isp but it didn't. Am I missing something > obvious? Can someone help me to get these files to work? > I've attached a simple xyz file to this message and the script that I've > been using is: > >
height=239 width=239 > startanim=true > animmode=ping > startspin=no > display3D=ball&stick > options3D=specular > frank=no > BGCOLOR="#000045" > name="co2 bend" > script="select all; rotate z-50; rotate y 25; rotate x 10;">
> > I hope that someone can explain what I need to do. thanks in advance > > Roma > > Roma E. Oakes > Postgraduate Student > School of Chemistry > The Queen's University of Belfast > David Keir Building > Stranmillis Rd > Belfast BT9 5AG > Tel: (+)44 (0)28 91821021 > Email: r.oakes@qub.ac.uk From chemistry-request@server.ccl.net Mon Mar 18 06:50:48 2002 Received: from 263.net ([202.96.44.45]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2IBoHp30428 for ; Mon, 18 Mar 2002 06:50:47 -0500 Received: by 263.net (Postfix, from userid 60001) id 9540F1C85B093; Mon, 18 Mar 2002 19:56:46 +0800 (CST) MIME-Version: 1.0 Message-ID: <3C95D5FE.00001B.17688@mta3> Date: Mon, 18 Mar 2002 19:56:46 +0800 (CST) From: "陈辉" To: chemistry@ccl.net Subject: =?gb2312?B?Y29udmVyZ2VuY2Ugb24gSVBDTQ==?= X-Priority: 3 X-Originating-IP: [218.2.137.48] X-Mailer: Coremail2.0 Copyright Tebie Ltd., 2001 Dear Sir: When I using IPCM in Gaussian98 to do single point calculation ,I find that the convergence of can not be reached. "the Largest difference in charges from previous cycle" do not change.My model is a hydrigen bond system.I use DFT method. what hint can you give me to solve the problem? thank you chenhui dept chemistry Nanjing univ P.R.China __________________________________________ 邮件到了吗?手机告诉你(http://mail.263.net/mmail/index.html) 点击下载95963上网直通车(http://www.263.net/0ji/StarDialer.exe) 我拿什么来诱惑你(http://95963.263.net/) 化妆品三折,香水半价(http://shopping.263.net/class004.htm) From chemistry-request@server.ccl.net Mon Mar 18 08:00:31 2002 Received: from MAIL.AD.Berry.edu ([66.20.28.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2ID0Vp31641 for ; Mon, 18 Mar 2002 08:00:31 -0500 Received: from [10.16.232.24] ([10.16.232.24]) by MAIL.AD.Berry.edu with Microsoft SMTPSVC(5.0.2195.4453); Mon, 18 Mar 2002 07:22:27 -0500 User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Mon, 18 Mar 2002 07:21:01 -0500 Subject: SUMMARY: A couple of questions about AIM analysis From: Gary Breton To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-OriginalArrivalTime: 18 Mar 2002 12:22:27.0420 (UTC) FILETIME=[911E59C0:01C1CE77] Hello all, I thank everyone for answering my question on AIM analysis. I was asked by some to post a summary, and so I am doing so. It would appear that the overall concensus is that the Gaussian implementation of AIM is not the most robust and that more specialized software is more appropriate (i.e., MORPHY, AIM2000, etc.). ************************* First, my original question: I have implemented AIM analysis from with Gaussian98W successfully many times. The keywords I use are: SCF(conver=8) density=current AIM=bondorders. The level of theory in all cases has been RB3LYP/6-311+G(2d,p) which is the same level of theory as the other calculations involving these molecules (e.g., minimizations, frequency calculations, NBO analysis). However,when attempting the same calculation on one particular structure, the calculation fails. I am given the information below: WARNING: RMS ERROR HAS INCREASED WARNING: RMS ERROR HAS INCREASED WARNING: RMS ERROR HAS INCREASED WARNING: RMS ERROR HAS INCREASED NEWTON STEP FAILED FOR SURFACE SHEET 16 Error termination via Lnk1e in C:\G98W\l609.exe. Job cpu time: 0 days 4 hours 16 minutes 8.0 seconds. File lengths (MBytes): RWF= 48 Int= 0 D2E= 0 Chk= 2 Scr= 1 The Gaussian User's Reference suggests that the AIM code will fail at times and cites the particular instance when the message NEWTON-RAPHSON STEP FAILED is due to a molecule with rings that has an unusual topology (which may well be the case). Is there any cure for this problem? Am I able to tweak something to get the calculation to go to completion? ******************** Don't know how to force gaussian to work round difficult topologies, but our in house code (MORPHY) is available for a modest fee and is it is easy adapt the internal settings to get round most problems [it will also look at the topology of the laplacian, and elf, and soon other fields like lol]. If you want any more info let me know. Richard Baders code (AIMPAC) is freely available and should be flexible enough to do what you want but I don't have any direct experience of it. regards noj Malcom ******************* We have done quite a bit of AIM recently but not using Gaussian. There have been several comments about the G98 AIM package that suggest that it is not robust, and will fail in cases like yours where there is extreme curvature in the atomic surfaces. I have heard of no "fix" for these cases. I believe that the G98 AIM package is essentially a re-packaging of the original AIMPAC bundle of Bader et al. We have found that the AIM2000 package has given us very good results, although the MORPHY program is also claimed to be very good and may in fact be superior if its long-awaited next version ever comes out. In several cases, atomic integrations attempted with the PROAIMV program from the AIMPAC bundle failed no matter what parameters we tried, but integration with AIM2000 succeeded. We have also found it much easier to enhance the accuracy of integrals with AIM2000. Good Luck. Phil Hultin ***************** The Gaussian implementation of AIM is not reknowned for its robustness. Their love affair ended a long time ago and the aim in gaussian is an old and not maintained version. I suggest using aim2000 or aimpac or morphy from a gaussian output wfn file. Yours, Alexandre HOCQUET *************** There is no known cure for this error. The program is attempting to fit a surface so it can do integration within the various regions. There are a number of topological features which cause it problems. The code is doing a first order search and this is obviously not high enough order but no one has taken on the task of implementing a higher order search, linear search etc, similar to what is done for difficult geometry optimization. There are a couple of bond order estimates in the NBO package. If you use # ... POP=NBORead and then after the structure add lines, $NBO BNDIDX NLMO $END you will see these printed out. If you need an estimate of the bond order better than something like Mulliken that is my recommendation. Douglas J. Fox Technical Support Gaussian, Inc. ******************* Dear Professor Gary Breton, Gaussian has a multiple of optimization and minimization methods. I think you are using the most default method, but I think there are other methods available, like QC, GDIIS, NODIIS, etc. I am not exactly sure where the error occurred because you cut off the output a little too short, but there are other methods. I am curious. Why do you use SCF(COVER=8)? The default I think is 7. Is there are a need for the extra accuracy in the SCF cycle for AIM calculations? Yours, Ha Yeon Cheong From chemistry-request@server.ccl.net Mon Mar 18 09:25:36 2002 Received: from c2bapps8.btconnect.com ([193.113.209.32]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2IEPap01191 for ; Mon, 18 Mar 2002 09:25:36 -0500 Received: from patriot (actually host host213-122-69-32.in-addr.btopenworld.com) by c2bapps8 with SMTP-CUST (XT-PP); Mon, 18 Mar 2002 14:25:24 +0000 From: "Roma Oakes" To: "ccl" Subject: *.xyz files Date: Mon, 18 Mar 2002 14:25:32 -0000 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Thanks to all who have replied so far. the consensus of opinion seems to be that the people in charge of the server need to add the MIME types. Now, getting through to them is proving to be another story altogether. They don't appear to have a dedicated phone no. or an email address, all I can do id keep phoning the support line in the hope of finding someone who will listen to me. If anyone has any other suggestions I'd be glad to hear them. Thanks Roma Roma E. Oakes Postgraduate Student School of Chemistry The Queen's University of Belfast David Keir Building Stranmillis Rd Belfast BT9 5AG Tel: (+)44 (0)28 91821021 Email: r.oakes@qub.ac.uk From chemistry-request@server.ccl.net Mon Mar 18 09:01:22 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2IE1Lp00573 for ; Mon, 18 Mar 2002 09:01:21 -0500 Received: from vega (sun250.divtlc.unimi.it [159.149.102.4]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0GT60070S9M2MY@mailstudenti.unimi.it> for chemistry@ccl.net; Mon, 18 Mar 2002 15:01:14 +0100 (MET) Date: Mon, 18 Mar 2002 15:01:47 +0100 From: Giulio Vistoli Subject: EGO - MD To: CCL Message-id: <005e01c1ce85$717eeb80$204f959f@farma.unimi.it.farma.unimi.it> Organization: Ist. Chimica Farmaceutica MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal Dear CCLers We would like to use EGO Molecular Dynamics program, but we are unable to compile the program for the Windows platform: there is someone that it has already compiled this software for Win-PCs? Thanks in advance Giulio Vistoli -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39 02 503 17522 Fax +39 02 503 17565 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Mon Mar 18 11:02:18 2002 Received: from gems.uia.ac.be ([143.169.254.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2IG2Ip03004 for ; Mon, 18 Mar 2002 11:02:18 -0500 Received: from uia.ua.ac.be (pcschc5.uia.ac.be [143.169.6.12]) by gems.uia.ac.be (8.11.6/8.11.6) with ESMTP id g2IG2Bf01728 for ; Mon, 18 Mar 2002 17:02:11 +0100 (MET) Message-ID: <3C960FF2.6D77B1@uia.ua.ac.be> Date: Mon, 18 Mar 2002 17:04:02 +0100 From: Anik Peeters Organization: University of Antwerp X-Mailer: Mozilla 4.78 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: plotting 3D electron density difference maps Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.5 Hi there, I am looking for software, preferably freeware, to plot 3D electron density or electron density difference maps for large molecules (appr. 500 atoms). The program may run on a unix workstation or on pc. We have our own programs to calculate the value of the electron density (difference) in the grid points of a given 3D lattice. Therefore, we can generate the results in any format needed, but we do need to know what the input format is for a given plotting program, so therefore we would prefer a program that comes along with its source code or sample input files. We also welcome programs for converting one 3D data set into another. I already donwloaded Molden, but it seems a bit slow when I am looking at our molecular system interactively. Friendly greetings, Dr. Anik Peeters University of Antwerp anik@uia.ac.be From chemistry-request@server.ccl.net Mon Mar 18 18:11:35 2002 Received: from mail.utexas.edu ([128.83.126.138]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2INBYp13328 for ; Mon, 18 Mar 2002 18:11:34 -0500 Received: (qmail 19078 invoked by uid 0); 18 Mar 2002 23:11:29 -0000 Received: from pc-rsp.phr.utexas.edu (HELO naphthyl.phr.utexas.edu) (128.83.164.142) by umbs-smtp-3 with SMTP; 18 Mar 2002 23:11:29 -0000 Message-ID: <3C96748E.B50D1F2E@naphthyl.phr.utexas.edu> Date: Mon, 18 Mar 2002 17:13:18 -0600 From: "Robert S. Pearlman" X-Mailer: Mozilla 4.75 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, qsar_society@msi.com Subject: Part 2 of ACS Symposium on Tautomerism and Protonation State ... Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello again -- It occurred to me that re-posting the abstract submission procedure might be a good idea but, while fishing it out of my "sent-mail" folder, I accidently sent the last message before it was finished. Sorry. > Please submit your abstract through the OASYS facility. Point your > browser to: http://oasys.acs.org/acs/224nm/comp/papers/index.cgi and > click the button for the "Tautomerism and Protonation State ..." Symposium. > Please be sure to follow the formatting instructions provided by OASYS. > 2. Please e-mail a copy of your abstract to me at > pearlman@list.phr.utexas.edu. REMEMBER, THE DEADLINE IS APRIL 1 AND I DO NOT HAVE THE AUTHORITY TO EXTEND IT! I look forward to receiving your abstract and seeing you in Boston (and Orlando)! Best wishes, -- 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 Mon Mar 18 17:00:19 2002 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2IM0Jp10730 for ; Mon, 18 Mar 2002 17:00:19 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.4712.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: plotting 3D electron density difference maps Date: Mon, 18 Mar 2002 13:59:59 -0800 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: plotting 3D electron density difference maps Thread-Index: AcHOreQ9lvZboKRlRVSQ9nR3OF2bLQAEdbyg From: "DeLano, Warren" To: "Anik Peeters" , Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g2IM0Jp10731 > From: Anik Peeters [mailto:anik@uia.ua.ac.be] > I am looking for software, preferably freeware, to plot 3D electron > density or electron density difference maps for large molecules (appr. > 500 atoms). The program may run on a unix workstation or on pc. PyMOL is ideal for this kind of project, where you might be able to do a bit of development in order to enable efficient transfer of your 3D dataset into the visualization program. http://www.pymol.org > We have our own programs to calculate the value of the > electron density > (difference) in the grid points of a given 3D lattice. > Therefore, we can > generate the results in any format needed, but we do need to know what > the input format is for a given plotting program, so > therefore we would > prefer a program that comes along with its source code or sample input > files. We also welcome programs for converting one 3D data set into > another. > PyMOL can read XPLOR and CCP4 format electron density files, but you can also create a 3D volume "brick" from within Python (using the high-perfomance "Numeric" package) to display volume data like electron density. Mesh isosurfaces are supported by the current binary release, and the impending release supports solid isosurfaces too (source code in current CVS). These are great for MO diagrams and/or electrostatic potential plots. Python is rapidly becoming a standard programming language for computational chemistry, so I encourage everyone to learn it. PyMOL's capabilities provide you with a specific reward for doing so. > I already donwloaded Molden, but it seems a bit slow when I am looking > at our molecular system interactively. Provided that you can access a graphics accelerator card, PyMOL's performance meets or beats any other package, and it is cross-platform (Windows, Unix, MacOSX). It can display any 3D map that will fit into available RAM. And now for the best part... PyMOL is unrestricted open-source software (even for commercial usage), meaning that it is free, modifiable, and redistributable in modified form. If you find PyMOL useful, then you are asked to help advance the project through development, documentation, or funding. PyMOL's users (hundreds of scientists distributed around the globe) are working together to make it a better and better package each and every day. Everyone is welcome to join the effort. The goal of PyMOL is to create the "Linux" of molecular modeling: a Python environment, (including PyMOL and other powerful packages), that is free, open-source, interoperable, and suited for an unlimited variety of tasks in computational chemistry and structural biology. - Warren PyMOL Founder -- mailto:warren@sunesis.com Warren L. DeLano, Ph.D. From chemistry-request@server.ccl.net Mon Mar 18 16:18:57 2002 Received: from mx.seanet.com ([199.181.164.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2ILIup09976 for ; Mon, 18 Mar 2002 16:18:57 -0500 Received: from Debug (ssl.seanet.com [199.181.164.13]) by mx.seanet.com (8.11.6/8.11.6) with SMTP id g2ILIip20926; Mon, 18 Mar 2002 13:18:44 -0800 (PST) Message-Id: <200203182118.g2ILIip20926@mx.seanet.com> To: Anik Peeters , chemistry@ccl.net From: Mark Thompson Subject: Re: CCL:plotting 3D electron density difference maps Date: Mon, 18 Mar 2002 13:18:48 US/Pacific X-Mailer: Endymion MailMan Professional Edition v3.0.35 Dear Anik, Pretty much all the modeling packages will render surfaces. ArgusLab (http://www.arguslab.com) will do what you ask. Currently ArgusLab recognizes two file formats for surface data: ArgusLab's own binary format and the Gaussian cube file format. If you can get the data into a cube file format, then you can import it into ArgusLab and do pretty much anything you like with it: combine it with other surface data, differences, maps, etc. Also, ArgusLab's contouring is very fast. For Gaussian cube files, ArgusLab will cache them so that you only have to read them in one time. The ArgusLab format is not proprietary and if you like we can confer off-line if you want the format. Reading ArgusLab's binary cube files is much faster than formatted reads of Gaussian cube files. ArgusLab is not free, but its very inexpensive for academic's. It runs on Windows based PCs. Cheers, Mark Thompson, PhD Planaria Software Seattle, WA > Hi there, > > I am looking for software, preferably freeware, to plot 3D electron > density or electron density difference maps for large molecules (appr. > 500 atoms). The program may run on a unix workstation or on pc. > > We have our own programs to calculate the value of the electron density > (difference) in the grid points of a given 3D lattice. Therefore, we can > generate the results in any format needed, but we do need to know what > the input format is for a given plotting program, so therefore we would > prefer a program that comes along with its source code or sample input > files. We also welcome programs for converting one 3D data set into > another. > > I already donwloaded Molden, but it seems a bit slow when I am looking > at our molecular system interactively. > > > Friendly greetings, > > Dr. Anik Peeters > University of Antwerp > anik@uia.ac.be > > > > -= 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 > > > > > > ======================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA http://www.arguslab.com ======================================= From chemistry-request@server.ccl.net Mon Mar 18 13:59:37 2002 Received: from linman.isisph.com ([204.255.125.131]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2IIxbp06837 for ; Mon, 18 Mar 2002 13:59:37 -0500 Received: from domino2.isisph.com (mail.isisph.com [10.1.1.5]) by linman.isisph.com (8.9.1/8.9.1) with ESMTP id KAA21615 for ; Mon, 18 Mar 2002 10:59:30 -0800 Subject: Conformational analysis of nucleosides To: chemistry@ccl.net X-Mailer: Lotus Notes Release 5.0.8 June 18, 2001 Message-ID: From: PDande@isisph.com Date: Mon, 18 Mar 2002 10:58:01 -0800 X-MIMETrack: Serialize by Router on Domino2/ISIS(Release 5.0.9a |January 7, 2002) at 03/18/2002 10:57:12 AM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Hi All! My question to you fellow CClers is as follows: I need to analyze (computationally) the conformations of various nucleosides, and ribonucleosides having modifications in the furanose and the heterocyclic base regions. Are you aware of any commercial and/ or shareware package that can achieve this. I will need to calculate atomic charges, assign proper atom properties and then perform molecular mechanics and dynamics simulations to assign determine the likely conformation of the molecules under study. A program that has the requisite force fields ( any suggestions for the proper force field to use would be appreciated), and should have reasonable cost and hardware requirements ( PC compatibility would be best). I look forward to the usual helpful responses and thank all respondents in advance. Sincerely, Prasad Dande ************************************************************************************************************************************************************** Prasad Dande, Ph. D. Senior Scientist Research Chemistry ISIS Pharmaceuticals 2292 Faraday Avenue Carlsbad, CA 92008 Tel: 760 603 4671 Fax: 760 603 4654 Prasad_Dande@isisph.com From chemistry-request@server.ccl.net Mon Mar 18 17:58:10 2002 Received: from mail.utexas.edu ([128.83.126.136]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2IMwAp12404 for ; Mon, 18 Mar 2002 17:58:10 -0500 Received: (qmail 11899 invoked by uid 0); 18 Mar 2002 22:58:02 -0000 Received: from pc-rsp.phr.utexas.edu (HELO naphthyl.phr.utexas.edu) (128.83.164.142) by umbs-smtp-2 with SMTP; 18 Mar 2002 22:58:02 -0000 Message-ID: <3C967167.F0E50A57@naphthyl.phr.utexas.edu> Date: Mon, 18 Mar 2002 16:59:51 -0600 From: "Robert S. Pearlman" X-Mailer: Mozilla 4.75 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, qsar_society@msi.com Subject: ACS Symposium on Tautomerism and Protonation States in the Context of Virtual Screening X-Priority: 1 (Highest) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues -- Something appears to have gone wrong! I thought that "Tautomerism and Protonation States in the Context of Virtual Screening" would be an excellent topic for a Symposium at the Boston ACS meeting and I expected that there would be numerous abstracts submitted. Thus, I was very surprised and disappointed when, upon returning to the US, I checked the ACS web-site and found that only one abstract (Keith & Catherine Davies') has been submitted!! I was about to contact the Chair of the COMP Division and suggest cancelling this Symposium but then noticed an e-mail from Yvonne Martin saying: > I was surprised to see that my talk was not scheduled. > Did I forget to send in the abstract? Given that Yvonne Martin is not the sort of person who forgets about submitting abstracts and given that the only abstract received was submitted back in February (before most people get around to it), it appears that there *may* have been some temporary problem with the abstract submission process. I submitted a test abstract just moments ago and it worked perfectly. IF YOU WANT TO PRESENT A PAPER AT THE AFOREMENTIONED SYMPOSIUM, PLEASE SUBMIT OR RESUBMIT YOUR ABSTRACT NOW!!! THE ACS DEADLINE (not mine!) IS APRIL 1ST. It might also be a good idea to send me a copy of your abstract. From chemistry-request@server.ccl.net Mon Mar 18 19:00:40 2002 Received: from rm-rstar.sfu.ca (root@[142.58.120.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2J00ep15079 for ; Mon, 18 Mar 2002 19:00:40 -0500 Received: from fraser.sfu.ca (johnsont@fraser.sfu.ca [142.58.101.25]) by rm-rstar.sfu.ca (8.10.1/8.10.1/SFU-5.0H) with ESMTP id g2J00O409884 for ; Mon, 18 Mar 2002 16:00:33 -0800 (PST) Received: from localhost (johnsont@localhost) by fraser.sfu.ca (8.9.2/8.9.2/SFU-5.0C) with ESMTP id QAA09933 for ; Mon, 18 Mar 2002 16:00:21 -0800 (PST) X-Authentication-Warning: fraser.sfu.ca: johnsont owned process doing -bs Date: Mon, 18 Mar 2002 16:00:21 -0800 (PST) From: Margaret Johnson To: chemistry@ccl.net Subject: AutoDock torsional restraints Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Just wondering if someone could suggest to me how to properly restrain torsion angles in AutoDock. I am trying to dock flexible ligands to a protein, using LGA, while applying restraints to allow only a small amount of flexibility in the torsion angles. When I use the command "hardtorcon", the program doesn't seem to apply a barrier at all. With "gausstorcon" and a barrier of 100 or more, there is a little flexibility but not enough. When I lowered the barrier to 10, it seemed to work at first, but later on I noticed a lot of conformations produced with torsional angles far outside the range. What are the units of this barrier and how/when is it applied in the calculation? Is this energy added to the internal energy of the ligand, or does it not appear in the final docked energies at all? And how can I get the program to show this penalty ("showtorpen" doesn't seem to work?) Any suggestions would be much appreciated. Thanks and best regards, Maggie Johnson Margaret A. Johnson Department of Chemistry Simon Fraser University Burnaby, B.C. Canada Tel: (604) 291-5650 Email: johnsont@sfu.ca