From chemistry-request@server.ccl.net Thu Oct 24 05:23:49 2002 Received: from fyserv1.fy.chalmers.se ([129.16.110.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9O9NnS01246 for ; Thu, 24 Oct 2002 05:23:49 -0400 Received: from fy.chalmers.se (ftf-pc32.fy.chalmers.se [129.16.112.162]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id LAA16846 for ; Thu, 24 Oct 2002 11:23:02 +0200 (MEST) Message-ID: <3DB7BC98.CB09CA19@fy.chalmers.se> Date: Thu, 24 Oct 2002 11:25:44 +0200 From: Patrik Johansson Organization: CTH X-Mailer: Mozilla 4.51 [sv] (Win98; I) X-Accept-Language: sv MIME-Version: 1.0 To: chemistry@ccl.net Subject: MC/sim-ann & Gamess Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CClers Has anyone tried to perform a MC/sim-ann calc within gamess using the globop routine _and_ using two different ab initio parts (i.e. not using efrag)? An example: to render starting positions for a Na+ ion around a large anionic molecule which itself is allowed to relax and the Na-anion interaction treated ab initio. Hints/examples anyone? I'll summarize the answers (if any) of course. best regards /Patrik -- Patrik Johansson (patrikj@fy.chalmers.se) Scientist @ Materials Physics Group Chalmers University of Technology 412 96 Goteborg SWEDEN NEW!!! http://fy.chalmers.se/mf/Computer.html http://fy.chalmers.se/~jpatrik/ From chemistry-request@server.ccl.net Thu Oct 24 03:41:00 2002 Received: from sina.com ([202.108.35.242]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g9O7exS31199 for ; Thu, 24 Oct 2002 03:40:59 -0400 Received: (qmail 7659 invoked by uid 99); 24 Oct 2002 07:36:24 -0000 Message-ID: <20021024073624.7657.qmail@sina.com> From: kzong To: chemistry@server.ccl.net Subject: MD simulations of DPPC bilayers MIME-Version: 1.0 Date: Thu, 24 Oct 2002 15:36:24 +0800 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 3 Content-Type: multipart/mixed; boundary="----------10354449847645SINAEMAIL---" This is a multi-part message in MIME format. ------------10354449847645SINAEMAIL--- Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain;charset="gb2312" Dear all: I wanted to apply CHARMM to do some MD simulations of DPPC bilayers. But I ment some difficulty in building the inital conformation. I used build-seq.inp(in attachment) to setup one dppc, but it counldn't produce the atom coordinates. Then I tried to use the conformation in support directory of charmm(support/membrane/dppc.tar.gz), but the format seemed imcompatible. I also searched the web to find a pre-equilibrated conformation. I found one(dppc_feller_feb99.crd) in http://www.psc.edu/general/software/packages/charmm/tutorial/mackerell/membrane.html But there didn't give more information of this conformation(details of the simulation). Anyone could give me some advice? Chen Hao =================================================================== ------------10354449847645SINAEMAIL--- Content-Disposition: inline;filename="build-seq.inp" Content-Transfer-Encoding: base64 Content-Type: application/x-msdownload; name="build-seq.inp" Qk9NQkxFViAtMQoKb3BlbiB1bml0IDEwIGNhcmQgcmVhZCBuYW1lIHRvcF9hbGwyN19saXBpZC5ydGYK cmVhZCBSVEYgY2FyZCB1bml0IDEwCmNsb3NlIHVuaXQgMTAKCm9wZW4gdW5pdCAxMCBjYXJkIHJlYWQg bmFtZSBwYXJfYWxsMjdfbGlwaWQucHJtCnJlYWQgUEFSQSBjYXJkIHVuaXQgMTAKY2xvc2UgdW5pdCAx MAoKcmVhZCBzZXF1IGNhcmQKMwpQQUxNIFBDR0wgUEFMTQogCmdlbmVyYXRlIGRwcGMgZmlyc3Qgbm9u ZSBsYXN0IG5vbmUgc2V0dXAKCnBhdGNoIGVzdDEgZHBwYyAyIGRwcGMgMQpwYXRjaCBlc3QyIGRwcGMg MiBkcHBjIDMKCmF1dG9nZW5lcmF0ZSBhbmdsZXMgZGloZWRyYWxzCgpvcGVuIHVuaXQgMSBjYXJkIHJl YWQgbmFtZSBkcHBjLnBkYgpyZWFkIGNvb3IgcGRiIHVuaXQgMQoKb3BlbiB3cml0ZSBmb3JtYXR0ZWQg dW5pdCAxMCBuYW1lIGRwcGMucHNmCndyaXRlIHBzZiBjYXJkIHVuaXQgMTAKY2xvc2UgdW5pdCAxMAoK Y29ucyBmaXggc2VsZWN0IC5ub3QuIGh5ZHJvZ2VuIGVuZAoKbWluaW1pemUgc2QgbnN0ZXAgNTAwIHRv bGVuciAwLjAxIC0KICAgICAgICAgY3V0bmIgMTQuMCByZGllIGVwcyAyLjAgdnN3aXRjaCBzaGlmdAoK Y29ucyBmaXggc2VsZWN0IHR5cGUgQyogLm9yLiB0eXBlIE4qIC5vci4gdHlwZSBPKiBlbmQKCm1pbmlt aXplIHNkIG5zdGVwIDUwMCB0b2xlbnIgMC4wMSAtCiAgICAgICAgIGN1dG5iIDE0LjAgcmRpZSBlcHMg Mi4wIHZzd2l0Y2ggc2hpZnQKCmNvbnMgZml4IHNlbGVjdCBub25lIGVuZAoKbWluaW1pemUgY29uaiBu c3RlcCA1MDAgdG9sZW5yIDAuMDEgLQogICAgICAgICBjdXRuYiAxNC4wIHJkaWUgZXBzIDIuMCB2c3dp dGNoIHNoaWZ0CgpvcGVuIHdyaXRlIGZvcm1hdHRlZCB1bml0IDEwIG5hbWUgZHBwY19taW5pbWl6ZWQu cGRiIAp3cml0ZSBzZXEgcGRiIHVuaXQgMTAKd3JpdGUgY29vciBwZGIgdW5pdCAxMApjbG9zZSB1bml0 IDEwCgpzdG9wCg== ------------10354449847645SINAEMAIL----- From chemistry-request@server.ccl.net Thu Oct 24 03:29:56 2002 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9O7TtS31045 for ; Thu, 24 Oct 2002 03:29:55 -0400 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Thu, 24 Oct 2002 09:29:54 +0200 Message-ID: <003501c27b2f$867ccb40$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: , References: <1035382218.3db6adca04dad@mail.unimo.it> Subject: Re: CCL:renumbering a pdb file Date: Thu, 24 Oct 2002 09:32:36 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 Hi, Mol2Mol can do such tricks: if a mol2 file is "scrambled", it corrects automatically the atoms. Or if you input a PDB file where the numbering is not progressive, the output will be OK. Anyway, could you send me such a Mol2 file to inspect it? Tamas ---------------------------------- Dr. Tamas E. Gunda Research Group for Antibiotics Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- From: To: Sent: Wednesday, October 23, 2002 16:10 Subject: CCL:renumbering a pdb file > > Hi everybody, > I have a problem related with the use of DOCK5.0. > The default output of the docking run is a mol2 file. > In order to visualize the output i need to convert this file to a pdb format. > I've have tried the conversion with Babel but the molecules in the pdb files > have not progressive numbers. > > Any suggestion? > > Thank you in advance. > > Sara > > Sara Pacchioni > PhD student > University of Modena e Reggio Emilia > Italy > e-mail: pacchioni.sara@unimore.it > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Oct 24 04:17:27 2002 Received: from wrzx35.rz.uni-wuerzburg.de ([132.187.3.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9O8HQS32249 for ; Thu, 24 Oct 2002 04:17:26 -0400 Received: from wrzx30.rz.uni-wuerzburg.de (wrzx30.rz.uni-wuerzburg.de [132.187.1.30]) by wrzx35.rz.uni-wuerzburg.de (8.8.8/8.8.8/uniwue-MM-1.05) with ESMTP id KAA30712; Thu, 24 Oct 2002 10:17:24 +0200 (MET DST) Received: from localhost (localhost [127.0.0.1]) by virusscan.rz.uni-wuerzburg.de (Postfix) with ESMTP id B75FD40E; Thu, 24 Oct 2002 10:17:24 +0200 (CEST) Received: from wrzx07.rz.uni-wuerzburg.de (wrzx07.rz.uni-wuerzburg.de [132.187.1.7]) by wrzx30.rz.uni-wuerzburg.de (Postfix) with ESMTP id A29CA3EF; Thu, 24 Oct 2002 10:17:24 +0200 (CEST) Received: from imap.uni-wuerzburg.de (wrzx31.rz.uni-wuerzburg.de [132.187.3.31]) by wrzx07.rz.uni-wuerzburg.de (Postfix) with ESMTP id 93E214FD; Thu, 24 Oct 2002 10:17:24 +0200 (CEST) Received: from localhost (wrzx32.rz.uni-wuerzburg.de [132.187.3.32]) by imap.uni-wuerzburg.de (Postfix) with ESMTP id EEE5F503; Thu, 24 Oct 2002 10:17:23 +0200 (CEST) Received: from 132.187.70.201 ( [132.187.70.201]) as user phar072@132.187.3.41 by webmail.uni-wuerzburg.de with HTTP; Thu, 24 Oct 2002 10:17:23 +0200 Message-ID: <1035447443.3db7ac93d4ff9@webmail.uni-wuerzburg.de> Date: Thu, 24 Oct 2002 10:17:23 +0200 From: Nikolaus Stiefl To: "Czerminski, Ryszard" Cc: "'Xiang Lu'" , reg8@cornell.edu, angelschnur@hotmail.com, chemistry@ccl.net Subject: Re: CCL:rotate molecules along princliple moments of inertia References: In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.0 X-Originating-IP: 132.187.70.201 X-Virus-Scanned: by AMaViS (Rechenzentrum Universitaet Wuerzburg) Hi all, we had a similar problem while implementing a new 3D molecular descriptor. What we do is at least fast to compute and I think rather straightforward. I am not sure whether or not this way is more rigorous but that's how we solve the problem: [1] centre the coordinate matrix X according to its mass. [2] determine the inertia tensor of this coordinate matrix [3x3]. Decompose the inertia tensor using singular value decomposition (or principal component analysis). The eigenvectors define the new coordinate system. [3] identify the determinant of the eigenvector matrix and if it is negative multiply the third eigenvector with -1 which changes the determinant to +1 (this way one makes sure to obtain a right-handed coordinate system). [4] Use this eigenvector matrix as rotation matrix for your coordinate matrix. Hope this helps, Nik -- Nikolaus Stiefl Chemometriks and Drug Design University Wuerzburg Dept. of Pharmacy Am Hubland D-97074 Wuerzburg Germany Phone: +49 - 931 8885473 Zitat von "Czerminski, Ryszard" : > It seems that the method described in the Kabsch paper is what you are > looking for: > > C Wolfgang Kabsch "A solution for the best rotation > C to relate two sets of vectors" Acta Cryst. (1976) A32, 922 > > R > > Ryszard Czerminski phone: (781)994-0479 > ArQule, Inc. email:ryszard@arqule.com > 19 Presidential Way http://www.arqule.com > Woburn, MA 01801 fax: (781)994-0679 > > > -----Original Message----- > From: Xiang Lu [mailto:xiangjun@rutchem.rutgers.edu] > Sent: Wednesday, October 23, 2002 11:15 AM > To: reg8@cornell.edu > Cc: angelschnur@hotmail.com; chemistry@ccl.net > Subject: CCL:rotate molecules along princliple moments of inertia > > > > You raised a good point and there are indeed some technical details to go > into to get things "right". While I am not so sure about the mathematics > and > physics involved, the procedures I used seem to work fine for my purpose: > > [1] Pre-process xyz (n-by-3 matrix) to reset its orientation according to > the reference frame of the first nucleic acid base; or as defined by > the > first 3 non-linear atoms. This will eliminate the ambiguity (e.g., > upside-down) associated with arbitrary initial orientation. > [2] get the co-variance matrix (real symmetric, 3-by-3). > [3] solve the eigensystem (using e.g. jacobi transformation as in Numerical > Recipes), sort the eigenvalues, and normalize eigenvectors. > [4] check to make sure the third eigenvector is the cross product of the > first two, otherwise reverse its sign. There are two more permutations > which can be used to get three orthogonal views. > > Does anyone out there have a more rigorous way? > > Xiang-Jun > > -- > Dr. Xiang-Jun Lu | Tel: (732) 445 4619 (O) > Department of Chemistry | > Rutgers University | Fax: (732) 445 5958 > 610 Taylor Road | Email: xiangjun@rutchem.rutgers.edu > Piscataway, NJ 08854-8087 | URL: http://rutchem.rutgers.edu/~xiangjun/ > > > >>>>> "Richard" == Richard Gillilan writes: > > Richard> This same problem pops up when I have an ensemble of > Richard> identical, but randomly-oriented bodies (proteins) > Richard> in solution and I wish to transform them all back to > Richard> - the same - body coordinate system. You get to the body > Richard> system by diagonalizing the inertial matix, but I suspect > Richard> the problem is that eigenvalues can be returned by the > Richard> numerical routine in any order and with any sign. The > Richard> resulting body coordinate sytems then differ by > Richard> permutations and sign changes of axes subject to the > Richard> condition that the handedness must be preserved. I seem > Richard> to remember this has something to do with permutation groups > Richard> so that the required sign changes are related to the > Richard> parity of the permutation (swap axes and you must change a sign > Richard> to preserve handedness). At any rate, is there a way of putting > Richard> eigenvectors in some kind of canonical order with appropriate > Richard> sign so that the diagonalization routines always land you in the > Richard> same body system? > > > Richard> Richard Gillilan > Richard> MacCHESS > > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > > From chemistry-request@server.ccl.net Thu Oct 24 05:08:18 2002 Received: from wrzx35.rz.uni-wuerzburg.de ([132.187.3.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9O98HS00857 for ; Thu, 24 Oct 2002 05:08:18 -0400 Received: from wrzx30.rz.uni-wuerzburg.de (wrzx30.rz.uni-wuerzburg.de [132.187.1.30]) by wrzx35.rz.uni-wuerzburg.de (8.8.8/8.8.8/uniwue-MM-1.05) with ESMTP id LAA01877 for ; Thu, 24 Oct 2002 11:08:17 +0200 (MET DST) Received: from localhost (localhost [127.0.0.1]) by virusscan.rz.uni-wuerzburg.de (Postfix) with ESMTP id 61A8B3DC for ; Thu, 24 Oct 2002 11:08:17 +0200 (CEST) Received: from wrzx07.rz.uni-wuerzburg.de (wrzx07.rz.uni-wuerzburg.de [132.187.1.7]) by wrzx30.rz.uni-wuerzburg.de (Postfix) with ESMTP id 5740E328 for ; Thu, 24 Oct 2002 11:08:17 +0200 (CEST) Received: from imap.uni-wuerzburg.de (wrzx31.rz.uni-wuerzburg.de [132.187.3.31]) by wrzx07.rz.uni-wuerzburg.de (Postfix) with ESMTP id 4B3D34D2 for ; Thu, 24 Oct 2002 11:08:17 +0200 (CEST) Received: from localhost (wrzx32.rz.uni-wuerzburg.de [132.187.3.32]) by imap.uni-wuerzburg.de (Postfix) with ESMTP id 3EF7F503 for ; Thu, 24 Oct 2002 11:08:17 +0200 (CEST) Received: from 132.187.70.201 ( [132.187.70.201]) as user phar072@132.187.3.41 by webmail.uni-wuerzburg.de with HTTP; Thu, 24 Oct 2002 11:08:17 +0200 Message-ID: <1035450497.3db7b88133e85@webmail.uni-wuerzburg.de> Date: Thu, 24 Oct 2002 11:08:17 +0200 From: Nikolaus Stiefl To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.0 X-Originating-IP: 132.187.70.201 X-Virus-Scanned: by AMaViS (Rechenzentrum Universitaet Wuerzburg) Hi, I am currently investigating a set of molecules of which two contain an iodine atom covalently bound to an aromatic ring. When running this dataset through GRID everything works fine except for the iodine containing structures. For both of them i get the following error message: (N970-W) SUSPECTED ERROR IN NUMBER OF COVALENTLY BOUND NEIGHBOURS, OR THE NUMBER OF NEIGHBOURS ONE PLACE REMOVED FROM HETATM: 8* 8 I <1> 1 Now, I checked the GRID-readable pdb file and it looks o.k to me. Therefore I just build iodbenzole in SYBYL (saved as mol2) and tried this with GREAT as well as GREATER which results again in the mentioned error message. To me the converted pdb file looks o.k. again :-(( I am sure someone already used GRID on iodine containing molecules so I hope this someone might be able to help me ... Cheers Nik -- Nikolaus Stiefl Chemometriks and Drug Design University Wuerzburg Dept. of Pharmacy Am Hubland D-97074 Wuerzburg Germany Phone: +49 - 931 8885473 From chemistry-request@server.ccl.net Thu Oct 24 03:22:39 2002 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9O7MZS30950 for ; Thu, 24 Oct 2002 03:22:39 -0400 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Thu, 24 Oct 2002 09:23:08 +0200 Message-ID: <002201c27b2e$94f017f0$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: "Alice NgarKit Ko" , References: Subject: Re: CCL:PDB file editing Date: Thu, 24 Oct 2002 09:25:51 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 Hi, Mol2Mol can do it. Have a look on: http://www.klte.hu/~gundat/m2m/index.html and navigate Main window, Edit menu or www.compuchem.com/mol2mol.htm Tamas ----- Original Message ----- From: "Alice NgarKit Ko" To: Sent: Wednesday, October 23, 2002 03:34 Subject: CCL:PDB file editing > Hi, > I would like to know if there is an easy way to edit a PDB file. I loaded > the structure into VMD for viewing. There are a lot of water molecules > that have traveled far from where I wanted them. I hope I can use some > program where I can just pick and delete the water molecules and then > write out the remaining atoms to a new PDB file. If anyone knows how to > do this, please let me know. Thank you very much > > Alice > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Oct 24 11:29:41 2002 Received: from mail.med.cornell.edu ([140.251.3.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9OFTfS08655 for ; Thu, 24 Oct 2002 11:29:41 -0400 Received: from cornell.edu ([140.251.122.57]) by mail.med.cornell.edu (Netscape Messaging Server 3.6) with ESMTP id AAA47032; Thu, 24 Oct 2002 11:29:40 -0400 Date: Thu, 24 Oct 2002 11:29:38 -0400 Subject: Re: CCL:MD simulations of DPPC bilayers Content-Type: text/plain; delsp=yes; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v546) Cc: chemistry@server.ccl.net To: kzong From: Simon Berneche In-Reply-To: <20021024073624.7657.qmail@sina.com> Message-Id: <68C51C38-E765-11D6-808B-0030653F9806@cornell.edu> Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.546) Chen, Which version of CHARMM are you using? The input that you attached is compatible with topology files of version c29 and newer. Starting with CHARMM c29, the topology file for lipids splits DPPC in sub-components: residues PALM and PCGL. Previous versions considered DPPC as a single residue. If you want to use the files in charmm's support/membrane directory you'll have to use the parameter and topology files included in there, which basically correspond to those distributed with CHARMM c26 to c28. Simon > Dear all: > I wanted to apply CHARMM to do some MD simulations of DPPC bilayers. > But I ment some difficulty in building the inital conformation. I used > build-seq.inp(in attachment) to setup one dppc, but it counldn't > produce the atom coordinates. Then I tried to use the conformation in > support directory of charmm(support/membrane/dppc.tar.gz), but the > format seemed imcompatible. I also searched the web to find a > pre-equilibrated conformation. I found one(dppc_feller_feb99.crd) in > http://www.psc.edu/general/software/packages/charmm/tutorial/ > mackerell/membrane.html > But there didn't give more information of this conformation(details of > the simulation). Anyone could give me some advice? > ____________________________________________ Simon BERNECHE B.R. Theoretical Biophysics Laboratory Weill Medical College of Cornell University email: simon.berneche@cornell.edu tel:(212)746-4237 fax: (212)746-4843 ____________________________________________ From chemistry-request@server.ccl.net Thu Oct 24 11:58:00 2002 Received: from ntsmtp01.usc.edu ([128.125.179.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9OFvxS09110 for ; Thu, 24 Oct 2002 11:57:59 -0400 Received: by NTSMTP01 with Internet Mail Service (5.5.2653.19) id ; Thu, 24 Oct 2002 08:57:59 -0700 Message-ID: From: "Pandey, Jaya" To: "'chemistry@ccl.net'" Subject: Drug designing Date: Thu, 24 Oct 2002 08:57:51 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear CCL, I am a starter in drug designing. I am a biologist. Can anyone tell me how Autodock 3.0 can be used for drug designing. I have certain molecules that I would like to dock on the receptor and select the criterias that would help me choose the inhibitors. Any guidelines and help would be appreciated. Thanks Jaya From chemistry-request@server.ccl.net Thu Oct 24 12:02:51 2002 Received: from ntsmtp01.usc.edu ([128.125.179.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9OG2pS09291 for ; Thu, 24 Oct 2002 12:02:51 -0400 Received: by NTSMTP01 with Internet Mail Service (5.5.2653.19) id ; Thu, 24 Oct 2002 09:02:51 -0700 Message-ID: From: "Pandey, Jaya" To: "'chemistry@ccl.net'" Subject: Mol2Mol Date: Thu, 24 Oct 2002 09:02:47 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear CCL, Can someone help me getting a freeware like Mol2Mol that can alter modify my molecule for receptor fit. Also, if we come across some molecule by designing what are the sources to get them synthesised for lab testing?? Jaya From chemistry-request@server.ccl.net Thu Oct 24 12:37:56 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9OGbuS10123 for ; Thu, 24 Oct 2002 12:37:56 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H4H003BNVIVIX@mailstudenti.unimi.it> for chemistry@ccl.net; Thu, 24 Oct 2002 18:37:43 +0200 (MEST) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0H4H003FZVIWJ2@smtp.unimi.it> for chemistry@ccl.net; Thu, 24 Oct 2002 18:37:45 +0200 (MEST) Date: Thu, 24 Oct 2002 18:38:44 +0200 From: Giulio Vistoli Subject: Re: CCL:Mol2Mol To: "Pandey, Jaya" , chemistry@ccl.net Message-id: <001a01c27b7b$d13e9a90$424f959f@Villa> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Mailer: Microsoft Outlook Express 6.00.2800.1106 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: Dear Jaya You can try VEGA program (http://www.ddl.unimi.it). This is as Mol2Mol but it is totally freeware. Giulio Vistoli ------ Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli@unimi.it http://www.ddl.unimi.it From chemistry-request@server.ccl.net Thu Oct 24 09:25:01 2002 Received: from ultra3000.if.sc.usp.br ([143.107.228.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9ODP0S05768 for ; Thu, 24 Oct 2002 09:25:00 -0400 Received: from if.sc.usp.br (floyd.ifqsc.sc.usp.br [143.107.228.51]) by ultra3000.if.sc.usp.br (8.11.6/8.11.0) with ESMTP id g9OCPEb02850; Thu, 24 Oct 2002 10:25:14 -0200 Message-ID: <3DB7E6F5.7010705@if.sc.usp.br> Date: Thu, 24 Oct 2002 10:26:29 -0200 From: Alexandre Suman de Araujo User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.1) Gecko/20020826 X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Czerminski, Ryszard" CC: "'Xiang Lu'" , reg8@cornell.edu, angelschnur@hotmail.com, chemistry@ccl.net Subject: Re: CCL:rotate molecules along princliple moments of inertia References: Content-Type: text/plain; charset=iso-8859-1; format=flowed Content-Transfer-Encoding: 8bit I developped a windows visual aplication using Kabsch algorithm... if it is interesting for you, send me a mail and I'll send you a copy. OK?? []'s Alexandre Suman de Araujo asaraujo@if.sc.usp.br UIN: 6194055 IFSC - USP - São Carlos - Brasil Czerminski, Ryszard wrote: >It seems that the method described in the Kabsch paper is what you are >looking for: > >C Wolfgang Kabsch "A solution for the best rotation >C to relate two sets of vectors" Acta Cryst. (1976) A32, 922 > >R > >Ryszard Czerminski phone: (781)994-0479 >ArQule, Inc. email:ryszard@arqule.com >19 Presidential Way http://www.arqule.com >Woburn, MA 01801 fax: (781)994-0679 > > >-----Original Message----- >From: Xiang Lu [mailto:xiangjun@rutchem.rutgers.edu] >Sent: Wednesday, October 23, 2002 11:15 AM >To: reg8@cornell.edu >Cc: angelschnur@hotmail.com; chemistry@ccl.net >Subject: CCL:rotate molecules along princliple moments of inertia > > > >You raised a good point and there are indeed some technical details to go >into to get things "right". While I am not so sure about the mathematics and >physics involved, the procedures I used seem to work fine for my purpose: > >[1] Pre-process xyz (n-by-3 matrix) to reset its orientation according to > the reference frame of the first nucleic acid base; or as defined by the > first 3 non-linear atoms. This will eliminate the ambiguity (e.g., > upside-down) associated with arbitrary initial orientation. >[2] get the co-variance matrix (real symmetric, 3-by-3). >[3] solve the eigensystem (using e.g. jacobi transformation as in Numerical > Recipes), sort the eigenvalues, and normalize eigenvectors. >[4] check to make sure the third eigenvector is the cross product of the > first two, otherwise reverse its sign. There are two more permutations > which can be used to get three orthogonal views. > >Does anyone out there have a more rigorous way? > >Xiang-JunI > > From chemistry-request@server.ccl.net Thu Oct 24 07:47:39 2002 Received: from mail.san.yahoo.com ([209.132.1.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9OBlcS03909; Thu, 24 Oct 2002 07:47:38 -0400 Received: from null (62.219.195.171) by mail.san.yahoo.com (6.5.029) id 3DB7C50C0000533D; Thu, 24 Oct 2002 04:35:50 -0700 Received: from 10.0.7.139 by null ([10.0.7.142] running VPOP3) with SMTP; Thu, 24 Oct 2002 13:38:44 +0200 Message-ID: <00de01c27b51$c32f0040$8b07000a@synergix.co.il> From: "Molecular Conceptor" To: "info" Subject: The first Drug Design Courseware Date: Thu, 24 Oct 2002 13:37:41 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00DB_01C27B62.8674ACC0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 X-Server: VPOP3 V1.5.0b - Registered This is a multi-part message in MIME format. ------=_NextPart_000_00DB_01C27B62.8674ACC0 Content-Type: text/plain; charset="windows-1255" Content-Transfer-Encoding: quoted-printable =20 Molecular Conceptor The first source of intelligent reference in Molecular Modeling & Drug = Design =20 =20 Dear Colleague, Recently, the scientific community was officially informed of the = availability of a courseware unique in its field, developed by the = education department of Synergix. 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------=_NextPart_000_00DB_01C27B62.8674ACC0-- From chemistry-request@server.ccl.net Thu Oct 24 17:29:43 2002 Received: from pauling.ncifcrf.gov ([129.43.6.78]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9OLTh515254 for ; Thu, 24 Oct 2002 17:29:43 -0400 Received: from localhost (liw@localhost) by pauling.ncifcrf.gov (SGI-8.9.3/8.9.3) with ESMTP id RAA93277 for ; Thu, 24 Oct 2002 17:21:39 -0400 (EDT) Date: Thu, 24 Oct 2002 17:21:39 -0400 From: Wen Li To: Subject: Dissipative Molecular Simulation In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All, Is there any available program for carrying out dissipative molecular simulations for macromolecules? Thanks, Wen From chemistry-request@server.ccl.net Thu Oct 24 14:14:28 2002 Received: from unq.edu.ar ([200.49.110.238]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9OIEPS12264 for ; Thu, 24 Oct 2002 14:14:26 -0400 Received: from pII400Win95.unq.edu.ar [200.49.110.129] by unq.edu.ar [200.49.110.238] with SMTP (MDaemon.PRO.v5.0.7.R) for ; Thu, 24 Oct 2002 15:08:15 -0300 Message-Id: <5.1.0.14.0.20021024151516.00a789d0@correo.unq.edu.ar> X-Sender: mlema@correo.unq.edu.ar X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 24 Oct 2002 15:15:27 -0300 To: chemistry@ccl.net From: =?iso-8859-1?Q?Mart=EDn?= Lema Subject: structure superposition source code Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed X-MDRemoteIP: 200.49.110.129 X-Return-Path: mlema@unq.edu.ar X-MDaemon-Deliver-To: chemistry@ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g9OIESS12265 Hello: Does anybody know of a free source code in c language to perform protein structure superposition by least squares fits? I need it to be as simple as possible, because I want to modify it in order to produce a superposition under special constrains (but I want to avoid programming the rotation and optimization algorithm). sincerely thanking in advance Martin Martín Lema Lic. en Biotecnología Universidad Nacional de Quilmes Roque Sáenz Peña 180 B1876BXD - Bernal Argentina Tel. +54 11 4365-7100 Tel./Fax. +54 11 4365-7132 Tel. Celular: +54 11 15-4530-4631 From chemistry-request@server.ccl.net Thu Oct 24 13:26:38 2002 Received: from wrzx35.rz.uni-wuerzburg.de ([132.187.3.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9OHQbS11447 for ; Thu, 24 Oct 2002 13:26:37 -0400 Received: from wrzx30.rz.uni-wuerzburg.de (wrzx30.rz.uni-wuerzburg.de [132.187.1.30]) by wrzx35.rz.uni-wuerzburg.de (8.8.8/8.8.8/uniwue-MM-1.05) with ESMTP id TAA30523 for ; Thu, 24 Oct 2002 19:26:37 +0200 (MET DST) Received: from localhost (localhost [127.0.0.1]) by virusscan.rz.uni-wuerzburg.de (Postfix) with ESMTP id DEAD648A for ; Thu, 24 Oct 2002 19:26:36 +0200 (CEST) Received: from wrzx37.rz.uni-wuerzburg.de (wrzx37.rz.uni-wuerzburg.de [132.187.3.37]) by wrzx30.rz.uni-wuerzburg.de (Postfix) with ESMTP id B4D78459 for ; Thu, 24 Oct 2002 19:26:36 +0200 (CEST) Received: from imap.uni-wuerzburg.de (wrzx31.rz.uni-wuerzburg.de [132.187.3.31]) by wrzx37.rz.uni-wuerzburg.de (Postfix) with ESMTP id A754C319 for ; Thu, 24 Oct 2002 19:26:36 +0200 (CEST) Received: from localhost (wrzx32.rz.uni-wuerzburg.de [132.187.3.32]) by imap.uni-wuerzburg.de (Postfix) with ESMTP id 9F057505 for ; Thu, 24 Oct 2002 19:26:36 +0200 (CEST) Received: from 132.187.70.201 ( [132.187.70.201]) as user phar072@132.187.3.41 by webmail.uni-wuerzburg.de with HTTP; Thu, 24 Oct 2002 19:26:36 +0200 Message-ID: <1035480396.3db82d4c8ef8d@webmail.uni-wuerzburg.de> Date: Thu, 24 Oct 2002 19:26:36 +0200 From: Nikolaus Stiefl To: chemistry@ccl.net Subject: Problem with iodine in GRID MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.0 X-Originating-IP: 132.187.70.201 X-Virus-Scanned: by AMaViS (Rechenzentrum Universitaet Wuerzburg) Sorry, forget the subject. Hope this is now better. Hi, I am currently investigating a set of molecules of which two contain an iodine atom covalently bound to an aromatic ring. When running this dataset through GRID everything works fine except for the iodine containing structures. For both of them i get the following error message: (N970-W) SUSPECTED ERROR IN NUMBER OF COVALENTLY BOUND NEIGHBOURS, OR THE NUMBER OF NEIGHBOURS ONE PLACE REMOVED FROM HETATM: 8* 8 I <1> 1 Now, I checked the GRID-readable pdb file and it looks o.k to me. Therefore I just build iodbenzole in SYBYL (saved as mol2) and tried this with GREAT as well as GREATER which results again in the mentioned error message. To me the converted pdb file looks o.k. again :-(( I am sure someone already used GRID on iodine containing molecules so I hope this someone might be able to help me ... Cheers Nik ---------------------- Nikolaus Stiefl Chemometriks and Drug Design University Wuerzburg Dept. of Pharmacy Am Hubland D-97074 Wuerzburg Germany Phone: +49 - 931 8885473