From chemistry-request@server.ccl.net Tue Nov 27 03:51:27 2001 Received: from rbadb2.rbacpxclu.bas.roche.com ([196.3.50.241]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAR8pQB03276 for ; Tue, 27 Nov 2001 03:51:26 -0500 Received: from CONVERSION-DAEMON.Roche.COM by Roche.COM (PMDF V6.0-025 #47170) id <01KB708C61E89AVATU@Roche.COM> for chemistry@ccl.net; Tue, 27 Nov 2001 09:47:12 +0100 Received: from rbamsemcn1.bas.roche.com (rbamsemcn1.bas.roche.com [145.245.211.139]) by Roche.COM (PMDF V6.0-025 #47170) with ESMTP id <01KB7086T7RW9AV76P@Roche.COM>; Tue, 27 Nov 2001 09:46:59 +0100 Received: by rbamsemcn1.bas.roche.com with Internet Mail Service (5.5.2653.19) id ; Tue, 27 Nov 2001 09:47:32 +0100 Content-return: allowed Date: Tue, 27 Nov 2001 09:47:23 +0100 From: "Borosy, Andras {Basi~Basel}" Subject: RE: Biopolymer modeling and Docking on windows NT To: "'PDande@isisph.com'" , chemistry@ccl.net Message-id: <5FBD82D1CB46D511AAEA0002A55C6F5202AAA92F@rbamsem3.bas.roche.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fAR8pRB03277 Dear Prasad, > > > I am looking for some information on available molecular > modeling software > for modeling of biopolymers > (proteins and nucleic acids) on the windows NT platform. I > need something > that is capable of performing basic > calculations on proteins and nucleic acids, including > protein-nucleic acid > docking operations. You may try Molecular Operating Environment of CCG! www.chemcomp.com Best regards, Borosy, András Basilea Pharmaceutica Ltd POB 3255, 65/316B 4002 Basel tel: +41-61-6885469 fax: +41-61-6882139 www.basileapharma.com From chemistry-request@server.ccl.net Tue Nov 27 06:06:28 2001 Received: from mailhost.curie.fr ([193.49.205.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fARB6SB05503 for ; Tue, 27 Nov 2001 06:06:28 -0500 Received: from mailhost.curie.fr (localhost [127.0.0.1]) by mailhost.curie.fr (8.11.6/jtpda-5.3.3) with ESMTP id fARB6Lc23558 for ; Tue, 27 Nov 2001 12:06:21 +0100 (MET) Received: from [10.20.10.167] (cm-1455-6659.curie.fr [10.20.10.167]) by mailhost.curie.fr (8.11.6/jtpda-5.3.3) with ESMTP id fARB6Ll23549 for ; Tue, 27 Nov 2001 12:06:21 +0100 (MET) Message-Id: Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Date: Tue, 27 Nov 2001 12:06:21 +0100 To: chemistry@ccl.net From: Emmanuel Bertounesque Subject: heterodiene with mopac Dear CCLers AM1 calculations (full geometry optimization) of the energies and Pz coefficients of the HOMO and the LUMO of the heterodiene 3-methylene-2,4-chromandione were reported by Appendino et al. (J. Org. Chem. 1994, 59, 5556-5564). As an exercise, I carried out the same calculations with the QCPE program MOPAC 6.0 (PRECISE, EF, full geometry optimization) implemented within SYBYL 6.5 and found differences of signs of the orbital coefficients. How to explain such a result? Did I forget an additional keyword? Thanking you in advance Dr Emmanuel Bertounesque From chemistry-request@server.ccl.net Tue Nov 27 05:46:49 2001 Received: from web12908.mail.yahoo.com ([216.136.174.75]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fARAknB05213 for ; Tue, 27 Nov 2001 05:46:49 -0500 Message-ID: <20011127104645.57168.qmail@web12908.mail.yahoo.com> Received: from [144.32.180.37] by web12908.mail.yahoo.com via HTTP; Tue, 27 Nov 2001 10:46:45 GMT Date: Tue, 27 Nov 2001 10:46:45 +0000 (GMT) From: =?iso-8859-1?q?Meike=20Reinhold?= Subject: B3LYP vs B3P86 To: chemistry MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Many thanks to all who replied to my e-mail last week, some people asked me to summarise the responses and here they are (order of appearance is totally arbitrary): 1.) Mark Saeys I know of two articles that compare different functionals for transition metal dimers, but I am not sure if they compare hybrid functionals-I know they conclude that pure functionals are more reliable than hybrid, because the HF part deteriorates the results. Homonuclear 3d transition-metal diatomics: A systematic density functional theory study, Barden, C.J., J.C. Rienstra-Kiracofe, H.F. Schaefer III, J. Chem. Phys.113(2), 690-700 (2000) An investigation of density functionals: The first-row transition metal dimer calculations, Yanagisawa S., T. Tsuneda, K. Hirao, J. Chem. Phys. 112: (2) 545-553 (2000) 2.) Marcel Swart there is a paper by Ulf Ryde (I think this year), in which he compares Becke-Perdew and B3LYP to MP2 geometries for model systems of the active site of type-1 copper proteins. I can't remember exactly in which journal etc., but I could look it up for you. I needed to look it up myself, so here is the ref: U. Ryde et al., Theor.Chem.Acc. (2001) 105:452-462 3.) RNDr. Jan Hrusak CSc. You may have a look to the papers published by us few years ago. I do not have them handy now, but if you look for some of the authors - i.e, Hrusak, Koch, Holthausen you will find most of them. 4.) Luis Antonio There are two papers that you might be interested: Chem. Phys. Letters 268 (1997) 345. J. Mol. Struct. (THEOCHEM) 430 (1998) 9. There you can find comparisons of B3LYP with other functionals. 5.) Per-Ola Norrby A good source would be "Computational Organometallic Chemistry", edited by Tom Cundari, avaliable from Marcel-Dekker. Specifically, chapter 4 by Diedenhofen, Wagener, and Frenking, does exactly the comparison you're asking for. You can find the book at this link: http://www.dekker.com/servlet/product/productid/0478-9 ===== Meike Reinhold Chemistry Department University of York UK __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From chemistry-request@server.ccl.net Tue Nov 27 09:46:12 2001 Received: from mail-02.med.umich.edu ([141.214.93.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAREkBB08814 for ; Tue, 27 Nov 2001 09:46:11 -0500 Received: from gwia-02-MTA by mail-02.med.umich.edu with Novell_GroupWise; Tue, 27 Nov 2001 09:46:07 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.1 Date: Tue, 27 Nov 2001 09:45:46 -0500 From: "Renxiao Wang" To: Subject: Database of complex structures? Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fAREkCB08815 Dear CCLers, I am looking for on-line databases which maintain a collection of all the complex structures from PDB. Basically a complete list is desired. If all the entries are organized in a logic way, that will be a major plus. I have checked "PDBSum" at http://www.biochem.ucl.ac.uk/bsm/pdbsum/ and "Relibase" at http://relibase.ebi.ac.uk/. Both of them provide some forms of useful information. I will appreciate it very much if anyone has other clues. I will certainly put back the summary. Regards, Renxiao Wang, Ph.D. University of Michigan Medical School From chemistry-request@server.ccl.net Tue Nov 27 11:35:46 2001 Received: from phm.utoronto.ca ([128.100.70.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fARGZjB11331 for ; Tue, 27 Nov 2001 11:35:45 -0500 Received: from phm.utoronto.ca (lpk04.phm.utoronto.ca [128.100.70.180]) by phm.utoronto.ca (8.9.3+Sun/8.9.3) with ESMTP id LAA19566 for ; Tue, 27 Nov 2001 11:35:41 -0500 (EST) Sender: william@phm.utoronto.ca Message-ID: <3C03C0E5.CC132D4A@phm.utoronto.ca> Date: Tue, 27 Nov 2001 11:35:49 -0500 From: William Wei Reply-To: william@phm.utoronto.ca Organization: Faculty of Pharmacy, U of T X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Any idea about spartan? Content-Type: multipart/alternative; boundary="------------5E8587803EDACF094A0CB4AA" --------------5E8587803EDACF094A0CB4AA Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, dear CCLers, Does anyone use spartan? Could you please give me some comments on the software compare to gaussian. I am now using the demo version of spartan, the support said it is full version with the time limit. While I do geometry optimization on my peptide-like compound under MP2/6-31G* or DF/DN*, if I constrain the dihedral angle of peptide (related) bone, then it seems the program went into a dead cycle, and did not give any further step energy output, or the energy became larger and larger. I do not know what wrong with it. Could anyone who have used the program give me some idea about that? Any reply is appreciated. Thanks, have a good day. William. -- William Wei Tel: 1-416-946-7551 (Lab.) Faculty of Pharmacy Fax: 1-416-978-8511 19 Russell Street Email: william@phm.utoronto.ca Toronto, ON. M5S 2S2, Canada william.wei@utoronto.ca --------------5E8587803EDACF094A0CB4AA Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, dear CCLers,

Does anyone use spartan? Could you please give me some comments on the software compare to gaussian. I am now using the demo version of spartan, the support said it is full version with the time limit. While I do geometry optimization on my peptide-like compound under MP2/6-31G* or DF/DN*, if I constrain the dihedral angle of peptide (related) bone, then it seems the program went into a dead cycle, and did not give any further step energy output, or the energy became larger and larger. I do not know what wrong with it. Could anyone who have used the program give me some idea about that? Any reply is appreciated.

Thanks, have a good day.

William. 

-- 
William Wei                    Tel: 1-416-946-7551 (Lab.)
Faculty of Pharmacy            Fax: 1-416-978-8511
19 Russell Street              Email: william@phm.utoronto.ca
Toronto, ON. M5S 2S2, Canada          william.wei@utoronto.ca
  --------------5E8587803EDACF094A0CB4AA-- From chemistry-request@server.ccl.net Tue Nov 27 19:31:49 2001 Received: from smtp3.jaring.my ([61.6.32.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAS0VkB23477 for ; Tue, 27 Nov 2001 19:31:46 -0500 Received: from vplaces.net (j187.crc21.jaring.my [61.6.158.201]) by smtp3.jaring.my (8.11.4/8.11.4) with ESMTP id fAS0VLl00965 for ; Wed, 28 Nov 2001 08:31:29 +0800 (MYT) Message-ID: <3C04305A.4B14B4AB@vplaces.net> Date: Wed, 28 Nov 2001 08:31:22 +0800 From: rowyna X-Mailer: Mozilla 4.75 [en] (Win98; U) X-Accept-Language: en,pdf MIME-Version: 1.0 To: CCL Subject: protocol for SA Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I'd like to perform a Monte Carlo simmulated annealing for some small ligands. I would be grateful if somebody can suggest a link as to where I might find a good protocol for performing the SA. I would like use discover or discover_3 in in insightII but somehow I can't seem to be able to generate the input files for simulated annealing. Any clues on how I can do it? I'll summarize the answers. Regards, Rowyna K. From chemistry-request@server.ccl.net Tue Nov 27 21:24:26 2001 Received: from mail.shcnc.AC.CN ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAS2OPB27388 for ; Tue, 27 Nov 2001 21:24:25 -0500 Received: from PC18 ([202.127.19.225]) by mail.shcnc.AC.CN (8.12.1/8.12.1) with SMTP id fASHMkVQ020922 for ; Wed, 28 Nov 2001 09:22:46 -0800 (PST) Message-Id: <200111281722.fASHMkVQ020922@mail.shcnc.AC.CN> Date: Wed, 28 Nov 2001 10:8:34 +0800 From: bxiong To: "chemistry@ccl.net" Subject: charmm parameter X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear CCLs: In my simulation, I find two abnormal residues in the protein. they are ASP and HIS protonation state. Can someone tell me about their charmm19 parameter? Thanks very much!! Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office)