From chemistry-request@server.ccl.net Wed Mar 28 07:58:06 2001 Received: from mailhub1.shef.ac.uk ([143.167.1.9]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2SCw6D31493 for ; Wed, 28 Mar 2001 07:58:06 -0500 Received: from ramsley.shef.ac.uk ([143.167.103.254]) by mailhub1.shef.ac.uk with esmtp (Exim 3.22 #2) id 14iFWW-0003sZ-00 for chemistry@ccl.net; Wed, 28 Mar 2001 13:58:04 +0100 Received: from RAMSLEY/SpoolDir by ramsley.shef.ac.uk (Mercury 1.48); 28 Mar 01 13:58:55 +0100 Received: from SpoolDir by RAMSLEY (Mercury 1.48); 28 Mar 01 13:58:44 +0100 From: "O.Nicolotti" To: chemistry@ccl.net Date: Wed, 28 Mar 2001 13:58:42 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: simoultaneous linear equations Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12a) Message-Id: Dear All, does anybody know where I can find some free C routines for solving simoultaneous linear equations for derive QSAR models? thanks, Orazio Orazio Nicolotti, PhD Research Associate Dept. Information Studies University of Sheffield Western Bank Sheffield S10 2TN tel. 0114 222 2651 From chemistry-request@server.ccl.net Wed Mar 28 09:14:10 2001 Received: from gwia.kvl.dk ([130.225.43.254]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f2SEE9D32043 for ; Wed, 28 Mar 2001 09:14:09 -0500 Received: from kvl.dk (pwt.kemi.kvl.dk [130.225.43.124]) by gwia.kvl.dk; Wed, 28 Mar 2001 16:07:07 +0200 Sender: pwt@ccl.net Message-ID: <3AC20DAB.ED997F43@kvl.dk> Date: Wed, 28 Mar 2001 16:13:31 +0000 From: "Peter W. Thulstrup" X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.4.0-4GB i686) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Specification of alpha and beta orbitals for g98 cube files? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear computational chemists! I am using gaussian 98 and would like visualize molecular orbitals with gOpenMol. In order to do this I first make a formated checkpoint file, whereafter I use cubegen to create cube files for each of the orbitals I want to display. A generic input for molecular orbital number 20 for cubegen could be: prompt:/cubegen 0 mo=20 molecule.fchk molecule_mo20.cube 40 h As I am doing calculations on open shell species, I would like to specify to cubegen, not only an orbital number, but also if it is an alpha or beta orbital. The input line above gives alpha orbital no. 20. Does the numbering of the beta orbitals simply start numerically after all occupied and virtual alpha orbitals? If anybody can help or maybe send me an example of an input-line that works for this purpose I will be very appreciative, Peter Peter W. Thulstrup Chemistry Department / Royal Veterinary and Agricultural University Thorvaldsensvej 40 / DK-1871 Frederiksberg C / Denmark E-mail: pwt@kvl.dk / Phone: +45 35282401 / Fax: +45 35282398 http://www.kemi.kvl.dk From chemistry-request@server.ccl.net Wed Mar 28 12:43:03 2001 Received: from localhost.localdomain (IDENT:root@[141.250.13.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2SHgvD00966 for ; Wed, 28 Mar 2001 12:43:02 -0500 Received: from tiscalinet.it (IDENT:mirco@cost [127.0.0.1]) by localhost.localdomain (8.11.0/8.11.0) with ESMTP id f2SHfn505468 for ; Wed, 28 Mar 2001 19:41:50 +0200 Sender: mirco@localhost.localdomain Message-ID: <3AC2225C.CBC31B3B@tiscalinet.it> Date: Wed, 28 Mar 2001 19:41:48 +0200 From: Mirco Meniconi X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16-22 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: charmm psf xplor Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hy all, I have to trasform a pdb file in a psf-xplor file using charmm program, but I have never used charmm. How have I to do? tanks in advance From chemistry-request@server.ccl.net Wed Mar 28 14:12:07 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2SJC7D01370 for ; Wed, 28 Mar 2001 14:12:07 -0500 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id OAA28639; Wed, 28 Mar 2001 14:12:07 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3AC234D9.453D62AE@cornell.edu> Date: Wed, 28 Mar 2001 14:00:42 -0500 From: Richard Wood X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Chem2Pac Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all Does anyone know whatever became of the program Chem2Pac, written by Marcio Cyrillo? I have copies on two of my pc's and I've reconfigured both of them (one accidentally, one on purpose) and I need to get new codes so I can use the program. I've done a web search and nothing comes up. Thanks, Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Wed Mar 28 10:59:58 2001 Received: from mail.iitk.ac.in ([210.212.54.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2SFxkD32725 for ; Wed, 28 Mar 2001 10:59:52 -0500 Received: from qasid.cc.iitk.ac.in (qasid.cc.iitk.ac.in [172.31.1.16]) by mail.iitk.ac.in (8.9.2/8.9.2) with ESMTP id VAA29390 for ; Wed, 28 Mar 2001 21:33:39 +0530 (IST) Received: from CHINMOY ([172.31.76.193]) by qasid.cc.iitk.ac.in (8.9.2/8.9.2) with SMTP id VAA12011 for ; Wed, 28 Mar 2001 21:19:22 +0530 (IST) Message-ID: <003901c0b79f$9af6ea10$c14c1fac@CHINMOY> From: "chinmoy ranjan" To: Subject: required a software to view the metal centre of a protein. Date: Wed, 28 Mar 2001 21:26:09 +0530 Dear CCLers, I am trying to see the exact architecture of active site of a protein . Could any one tell me any software or tool (preferably free )through which I could view the exact metal centre of the protein. I tried to edit the PDB file and view the metal centre using rasmol but without much success. Thanks in advance. CHINMOY RANJAN INDIAN INSTITUTE OF TECHNOLOGY KANPUR From chemistry-request@server.ccl.net Wed Mar 28 15:43:22 2001 Received: from fulcrum.physbio.mssm.edu ([146.203.4.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2SKhLD01849 for ; Wed, 28 Mar 2001 15:43:21 -0500 Received: from mezei (helo=localhost) by fulcrum.physbio.mssm.edu with local-esmtp (Exim 3.11 #1) id 14iMmT-00CtHC-00; Wed, 28 Mar 2001 15:43:01 -0500 Date: Wed, 28 Mar 2001 15:43:01 -0500 From: Mihaly Mezei X-Sender: mezei@fulcrum.physbio.mssm.edu To: chinmoy ranjan cc: CHEMISTRY@ccl.net Subject: Re: CCL:required a software to view the metal centre of a protein. In-Reply-To: <003901c0b79f$9af6ea10$c14c1fac@CHINMOY> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: Mihaly Mezei Greetings, The program Ligplot from the Thorton lab prepares a nice schematic drawing in 2D showing the protein environment of a ligand (reading the info from a PDB file). The URL I have (it is olda - may have been changed) is http://www.biochem.ucl.ac.uk/~mcdonald/ Mihaly Mezei, Dept. of Physiology & Biophysics, Mount Sinai School of Medicine Voice: (212) 241-2186 Fax: (212) 860-3369| WWW: http:// adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01 From chemistry-request@server.ccl.net Wed Mar 28 15:37:49 2001 Received: from web13202.mail.yahoo.com ([216.136.174.187]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f2SKbmD01826 for ; Wed, 28 Mar 2001 15:37:49 -0500 Message-ID: <20010328203748.89934.qmail@web13202.mail.yahoo.com> Received: from [129.105.55.29] by web13202.mail.yahoo.com; Wed, 28 Mar 2001 12:37:48 PST Date: Wed, 28 Mar 2001 12:37:48 -0800 (PST) From: mike smith Subject: Any tip for a theoretical graduate to find a job? To: chemistry@ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, As a graduate student on theoretical chemistry, I am thinking of future empolyment opportunity. However, as we all know that it is very tough to get a job in industry for a person like me, but I am still curious to give a try. Hope someone in the list could be kind to provide any tip to save me out of school. :-) BTW, do we have to go for a postdoc in an industry-closely-related group for another couple of years? Maybe that would be my best choice, but I am a bit afraid that they may not accept application from my background... Life is just too tough! :-) PS: I am kind of pure theoretical guy, and almost know nothing about QSAR, drug-design, dock/lead stuff... which have been occupying the ad places of "Chemical & Engineering News" or CCL-job... PPS:how long does it take to learn those stuff? Should it be more easy than Schrodinger Equation...? Thanks a lot! --Mike __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/?.refer=text From chemistry-request@server.ccl.net Wed Mar 28 22:41:55 2001 Received: from smtp1.ndsu.nodak.edu ([134.129.111.146]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2T3ftD03221 for ; Wed, 28 Mar 2001 22:41:55 -0500 Received: from hotmail.com (sud8b.pharm.ndsu.NoDak.edu [134.129.118.52]) (authenticated (0 bits)) by smtp1.ndsu.nodak.edu (8.11.2/8.11.2) with ESMTP id f2T3fWf25548; Wed, 28 Mar 2001 21:41:32 -0600 Message-ID: <3AC2AEED.A8E91DC9@hotmail.com> Date: Wed, 28 Mar 2001 21:41:33 -0600 From: xin_hu Organization: NDSU X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: "Garrett M. Morris" CC: "art'" , Prashant Desai , CCL , Arthur Olson , David Goodsell , Michel Sanner Subject: Re: CCL:Announcing AutoDock 3.0.5 GUI: AutoDockTools, ADT References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I am very glad to know the ADT and download it. But when I try to run it, it always show an error like that: Traceback (most recent call last): File "./adt', line 40, in? import AutoDockTools Import Error: No module named Autodocktool I do not how the module or python works. DO I need do some other installation in order to start adt or pmv script (such as link with AUTODOCK3.0)? Thank you very much for your instruction. xin hu "Garrett M. Morris" wrote: > Dear Prashant, > > With the release of AutoDockTools, also known as 'ADT', AutoDock has > become more self-sufficient than ever. ADT provides a graphical user > interface to set up the ligand PDBQ file, the AutoGrid grid maps, the > AutoDock docking parameters, the ability to launch docking jobs, and > the ability to read in and analyse DLG AutoDock docking log files. You > can visualize isocontoured AutoGrid maps for atomic affinity and > electrostatice potential, and compute and display molecular surfaces. > > Babel has been ported into ADT, so its Gasteiger partial atomic charge > calculation method is available for small molecules, and there is also > the ability to assign Kollman united-atom charges to > proteins. Previously, you would have needed SYBYL to do this. > > You can also assign solvation parameters to a macromolecule, and > perform operations like adding hydrogens and merging non-polar > hydrogens, or detecting aromatic carbons (necessary for solvation > parameters). > > ADT is free for non-commercial applications, and is available from Art > Olson's Molecular Graphics Laboratory web site - click on Python > Software Development's "Related links", then "Downloads" > > http://www.scripps.edu/pub/olson-web/index.html > > After you have accepted the license agreement and registered (free), > click the radio button "Download Python packages" and then click > "Start". > > Currently supported platforms are: > > SGI IRIX 6.2 or higher, R4000 or better > Intel Linux 2 > Sun Sun OS 5 > > Coming soon: > > Windows > Mac OS X 10.0 > > You can select all the packages you want and the packager will tar > everything you need into one downloadable file. Just check the > "AutoDockTools" check-box and then click "Select dependent > packages". The packager determines any dependencies for you. > > On Fri, 23 Mar 2001, art' wrote: > > > Hi Desai, > > > > AutoDock has almost all software to make docking, with exception : > > 1. To visualize the structures in PDB (the results) 2.To create > > PDBQ file for ligand and macromolecule (add charges to PDB > > format). Of course, here we need some force field to calculate > > charges ....... > > > > The latest thing make the most inconvenience to prepare jobs ... > > And 'addsol' crashes while converting PDBQ to PDBQS file. Here > > Email Ruth Huey if you have problems with "addsol" - her email address > is rhuey@scripps.edu; this may have already been fixed in the > currently released tar file. > > > I've wrote my own win32 application. > > > > I don't know about DOCK, but AutoDock have rised some doubts about > > flexible docking. If anybody has the experience of flexible > > docking with AotoDock 3.0, it would be nice if one could share > > his/her comments about that . :) > > Take a look at the paper in the Journal of Computational Chemistry > comparing Simulated Annealing, Genetic Algorithm and Lamarckian > Genetic Algorithm in AutoDock 3.0: > > Morris, G. M., Goodsell, D. S., Halliday, R.S., Huey, R., Hart, > W. E., Belew, R. K. and Olson, A. J. (1998), J. Computational > Chemistry, 19: 1639-1662. > "Automated Docking Using a Lamarckian Genetic Algorithm and and > Empirical Binding Free Energy Function". > > AutoDock's web site is at: > > http://www.scripps.edu/pub/olson-web/doc/autodock/ > > For more information and a list of peer-reviewed publications, click > on "References". > > > > > have a good day > > A.Ziemys > > > > > > Prashant Desai wrote: > > > > > I tried understanding DOCK and I realized that one requires 'MS' from > > > QCPE to generate molecular surfaces. Since I don't have 'MS' can anybody > > > suggest some way out? > > > How about using Autodock? Is it self sufficient or even it requires use > > > of some additional softwares? > > > I am also looking for performance comparison of 'Affinity' from MSI with > > > other docking packages. I have not come across as many references on use > > > of Affinity as those for either DOCK or Autodock. Can anyone send me a > > > list of articles where Affinity has been utilized or even compared with > > > other docking softwares? > > > Thanking in advance. > > > Prashant Desai > > > > > > > > > Happy docking! > > Garrett > > ___ > Dr Garrett M. Morris, MA, DPhil > The Scripps Research Institute, tel: (858) 784-2292 > Dept. Molecular Biology, MB-5, fax: (858) 784-2860 > 10550 North Torrey Pines Road, email: garrett@scripps.edu > La Jolla, CA 92037-1000, USA. www.scripps.edu/pub/olson-web/gmm > > -= 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 -- ************************************************* Xin Hu Department of Pharmaceutical Science College of Pharmacy North Dakota State University Fargo, ND 58105 Tel: 701-231-8298 (O) 701-231-4360 (H) Fax: 701-231-7781 E-mail: Xin_Hu@ndsu.nodak.edu xxh0541@hotmail.com ************************************************* From chemistry-request@server.ccl.net Wed Mar 28 22:47:48 2001 Received: from smtp1.ndsu.nodak.edu ([134.129.111.146]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2T3lmD03237 for ; Wed, 28 Mar 2001 22:47:48 -0500 Received: from hotmail.com (sud8b.pharm.ndsu.NoDak.edu [134.129.118.52]) (authenticated (0 bits)) by smtp1.ndsu.nodak.edu (8.11.2/8.11.2) with ESMTP id f2T3llf25631; Wed, 28 Mar 2001 21:47:47 -0600 Message-ID: <3AC2B06C.6E66E7ED@hotmail.com> Date: Wed, 28 Mar 2001 21:47:56 -0600 From: xin_hu Organization: NDSU X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, xin_hu@ndsu.nodak.edu Subject: Re: CCL:about FT Dock References: <3AC0A814.5040307@bom2.vsnl.net.in> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers: I appreciate if someone can tell me how the MakeLaunch program in AUTODOCK3.0 works. What's the hostname need save in "cluster"? I try to do library screening using AUTODOCK, I wonder the MakeLaunch can do it. Thanks for you kind help. xin -- ************************************************* Xin Hu Department of Pharmaceutical Science College of Pharmacy North Dakota State University Fargo, ND 58105 Tel: 701-231-8298 (O) 701-231-4360 (H) Fax: 701-231-7781 E-mail: Xin_Hu@ndsu.nodak.edu xxh0541@hotmail.com *************************************************