From chemistry-request@server.ccl.net Tue May 14 08:28:24 2002 Received: from mail1.servers.anterio.com ([212.65.26.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4ECSNg03533 for ; Tue, 14 May 2002 08:28:23 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by mail1.servers.anterio.com (Postfix) with ESMTP id 0DB30ADD; Tue, 14 May 2002 14:28:23 +0200 (CEST) Received: from localhost.localdomain (anterio.internal.anterio.com [192.168.1.10]) by mail1.servers.anterio.com (Postfix) with ESMTP id 4D3C4ACE; Tue, 14 May 2002 14:28:22 +0200 (CEST) Received: (from gerd@localhost) by localhost.localdomain (8.11.6/8.11.6) id g4ECSER02301; Tue, 14 May 2002 14:28:14 +0200 Date: Tue, 14 May 2002 14:28:14 +0200 Message-Id: <200205141228.g4ECSER02301@localhost.localdomain> X-Authentication-Warning: localhost.localdomain: gerd set sender to gerd@anterio.com using -f From: Gerd Raether To: uccatvm@ucl.ac.uk Cc: chemistry@ccl.net, T.vanMourik@ucl.ac.uk In-reply-to: <200205132056.g4DKuhe03012@socrates-a.ucl.ac.uk> (message from uccatvm on Mon, 13 May 2002 21:56:43 +0100 (BST)) Subject: Re: CCL:counterpoise with LMP2 References: <200205132056.g4DKuhe03012@socrates-a.ucl.ac.uk> X-Virus-Scanned: by AMaViS perl-11 Hi Tanja, maybe the work of Istvan Mayer et al. author = {I. Mayer and \'A. Vib\'ok and G. Hal\'asz and P. Valiron}, title = {A BSSE-Free SCF Algorithm for Intermolecular Interactions. III. Generarlization for Three-Body Systems and for Using Bond Functions}, journal = {Int. J. Quantum Chem.}, year = {1996}, volume = {57}, pages = {1049} (see also the references there) is useful for you. This approach is especially useful if you are going to use small basis sets. Here you also get a BSSE free wave function. Furthermore as far as I know you will find also a discussion how the classical Boys Bernardi Method should be applied - this should be sufficient if you just go for BSSE free energies. Gerd From: uccatvm Date: Mon, 13 May 2002 21:56:43 +0100 (BST) Hi all, I am wondering what the most correct way is to do counterpoise with local MP2. In the local MP2 method originally proposed by Pulay (Chem.Phys.Lett. 100, 151, 1983), to each localised MO a subset (orbital domain) of the virtual orbitals is assigned. To calculate the interaction energy of a weakly interacting system, the orbital domains of the subsystems are first determined at large distance, and used in subsequent dimer calculations at smaller intermolecular distances (as recommended in for example Schutz et al., J. Phys. Chem. 102, 5997, 1998). Now, I assume that (to keep a true counterpoise) it is best to use the orbital domains determined at large distance for the monomer+ghost calculation. For this, one would first have to determine the domains of the monomer+ghost with the ghost at large R, and use the thus obtained orbital domains in the monomer+ghost calculation at the smaller distance. What do people think? Would this be the correct way of doing it? Of course, the BSSE is strongly reduced in LMP2, and should in principle be negligible when using an appropriate basis set. However, when using small basis sets it may not be negligible, and I would like to know the best way of doing counterpoise for these cases. Thanks in advance, Tanja -- ===================================================================== Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik@ucl.ac.uk London WC1H 0AJ, UK home: tanja@netcomuk.co.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html ===================================================================== -= 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 Tue May 14 06:03:38 2002 Received: from web14603.mail.yahoo.com ([216.136.224.83]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4EA3cg01215 for ; Tue, 14 May 2002 06:03:38 -0400 Message-ID: <20020514100337.51019.qmail@web14603.mail.yahoo.com> Received: from [203.87.132.164] by web14603.mail.yahoo.com via HTTP; Tue, 14 May 2002 11:03:37 BST Date: Tue, 14 May 2002 11:03:37 +0100 (BST) From: =?iso-8859-1?q?amor=20san=20juan?= Subject: Wanted: freeware for ligand preparation To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit CLLers: Do you know a freeware used in ligand preparation that is capable of adding charge & implicit Hydrogens exported as mol2 Sybyl file built in one package program? Please let me know.Thanks in advance. Amor UP-Diliman Philippines __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From chemistry-request@server.ccl.net Tue May 14 10:04:09 2002 Received: from citrin.chemie.uni-dortmund.de ([129.217.221.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4EE46g05402 for ; Tue, 14 May 2002 10:04:09 -0400 Received: from chemie.uni-dortmund.de (unknown [129.217.221.9]) by citrin.chemie.uni-dortmund.de (Postfix) with ESMTP id DCB211DA039 for ; Tue, 14 May 2002 16:03:56 +0200 (CEST) Message-ID: <3CE11953.B11E62F5@chemie.uni-dortmund.de> Date: Tue, 14 May 2002 16:04:03 +0200 From: dck X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: de,en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:how to suppress the standard orientation in G98? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit hello! how can i suppress the standard orientation in G98, and force g98 to calculate the molecules properties in the geometry, given in the input? or in other words, what's the keyword or iop corresponding to the coord=unique in GAMESS. yours dc kleb From chemistry-request@server.ccl.net Tue May 14 03:02:43 2002 Received: from web2.up.edu.ph ([64.94.101.194]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4E72dg29032 for ; Tue, 14 May 2002 03:02:39 -0400 Received: (qmail 22955 invoked by uid 504); 14 May 2002 07:25:13 -0000 Received: from amor_sanjuan@yahoo.com by web2 with qmail-scanner-1.01 (update: v4202 08 May 2002. Clean. Processed in 0.403989 secs); 14 May 2002 07:25:13 -0000 Received: from unknown (HELO b01.mail.up.edu.ph) (10.16.3.1) by 10.16.3.144 with SMTP; 14 May 2002 07:25:12 -0000 Received: (qmail 19766 invoked from network); 14 May 2002 07:05:26 -0000 Received: from unknown (HELO localhost) ([10.16.3.5]) (envelope-sender ) by 10.16.3.1 (qmail-ldap-1.03) with SMTP for ; 14 May 2002 07:05:26 -0000 Received: from 10.32.129.44 ( [10.32.129.44]) as user aasanjuan@b03.mail.up.edu.ph by mail.up.edu.ph with HTTP; Tue, 14 May 2002 15:08:40 +0800 Message-ID: <1021360120.3ce0b7f8a9c1b@mail.up.edu.ph> Date: Tue, 14 May 2002 15:08:40 +0800 From: amor san juan To: chemistry@ccl.net Subject: Ligand preparation 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: 10.32.129.44 Dear AutoDocker's community: Can someone recommend any other softwares for ligand preparation (aside from chemskestch5, babel &/or ADT). I need your help. Using Chemsketch5 I draw the benzamidine(ben.mol) structure then, used Babel to add explicit hydrogens & ben.mol2 conversion. The result is flawed ben.pdbq file as viwed below: REMARK 2 active torsions (identified by new id numbers): REMARK status: ('A' for Active; 'I' for Inactive) REMARK I 3- 7 between atoms: C3 and C7 REMARK 1 A 7- 8 between atoms: C7 and N1 REMARK 2 A 7- 10 between atoms: C7 and N2 ROOT ATOM 1 A1 <1> 1 -4.129 2.188 0.000 0.00 0.00 0.000 2 ATOM 2 A2 <1> 1 -4.129 1.362 0.000 0.00 0.00 0.000 2 ATOM 3 A3 <1> 1 -3.417 0.954 0.000 0.00 0.00 0.000 3 ATOM 4 A4 <1> 1 -2.705 1.362 0.000 0.00 0.00 0.000 2 ATOM 5 A5 <1> 1 -2.705 2.188 0.000 0.00 0.00 0.000 2 ATOM 6 A6 <1> 1 -3.417 2.604 0.000 0.00 0.00 0.000 2 ATOM 7 C7 <1> 1 -3.417 0.129 0.000 0.00 0.00 0.000 3 ENDROOT BRANCH 7 8 ATOM 8 N1 <1> 1 -4.132 -0.283 0.000 0.00 0.00 0.000 2 ATOM 9 H6 <1> 1 -5.107 -0.581 0.000 0.00 0.00 0.000 1 ENDBRANCH 7 8 BRANCH 7 10 ATOM 10 N2 <1> 1 -2.703 -0.283 0.000 0.00 0.00 0.000 3 ATOM 11 H7 <1> 1 -2.703 -1.303 0.000 0.00 0.00 0.000 1 ATOM 12 H8 <1> 1 -1.819 0.227 0.000 0.00 0.00 0.000 1 ENDBRANCH 7 10 TDOF 3 ------------------ Diagramatically, the steps I did to prepare ligand is: ben.mol -----> ben.mol2 ---------> ben.pdbq babel autotors3 Alternatively, I used ADT yet, the same zeros in last columns appeared (no charge present). Amor From chemistry-request@server.ccl.net Tue May 14 04:04:55 2002 Received: from post.webmailer.de ([192.67.198.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4E84sg31258 for ; Tue, 14 May 2002 04:04:54 -0400 Received: from fepa.biop.ox.ac.uk (fepa.biop.ox.ac.uk [163.1.16.72]) by post.webmailer.de (8.9.3/8.8.7) with ESMTP id KAA13708 for ; Tue, 14 May 2002 10:04:49 +0200 (MET DST) Message-Id: <200205140804.KAA13708@post.webmailer.de> X-Mailer: exmh version 2.3.1 01/18/2001 (debian 2.3.1-1) with nmh-1.0.2 To: CHEMISTRY@ccl.net Subject: Charge scaling for implicit solvent calculations X-image-url: http://crypt.u-strasbg.fr/marc/m-baaden.gif X-url: X-Face: -Nz&SN]%I8g9WFR#/!fe9se!_G_OndNloj@t+6jrGsoZ"z)?an0n P!Nls~*o?u7fy:]1N|^^(KX*uE>Nk{bHaCJ)(hXF~E#5)j.k0n4hgfIzpmn,[VY'\7X:;VOZ\CItIq G!2f8,k2`VLrkXQ:<.3LxEQ'E-;d:A)V# Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Tue, 14 May 2002 09:04:00 +0100 From: Marc Baaden Dear colleagues, I am trying to get hold of a sound reference, providing a rationale for scaling the charges of ionized groups when doing implicit solvent calculations (MM, MD, NMA) with eg epsilon=80 or epsilon=f(r). I am roughly aware of the counterion condensation theory of Manning and related work, but am not sure whether this is the only argument for charge scaling. Scaling factors (for proteins !) that I have seen in the literature seem to be around eg 0.3. How are they derived (ad hoc ? or by using the Xi=1 relation of Manning and calculating the charge density of the molecule). Also Manning's work focused on simple cylindrical models of polyions, but I am particularly interested in proteins. Is there any work focusing on this problem ? Thanks in advance, Marc Baaden -- Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University mailto:baaden@smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de FAX/Voice +49 697912 39550 - Tel: +44 1865 275380 or +33 609 843217 From chemistry-request@server.ccl.net Tue May 14 10:29:56 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4EETtg06158 for ; Tue, 14 May 2002 10:29:56 -0400 Received: from CONVERSION-DAEMON.unisi.it by unisi.it (PMDF V6.0-24 #43309) id <01KHQ38MMMK00031Z7@unisi.it> for chemistry@ccl.net; Tue, 14 May 2002 16:29:48 +0100 (MET) Received: from zeus (sysbiotech.bio-mol.unisi.it [192.167.124.8]) by unisi.it (PMDF V6.0-24 #43309) with ESMTP id <01KHQ38LGKXM002YAH@unisi.it> for chemistry@ccl.net; Tue, 14 May 2002 16:29:46 +0100 (MET) Date: Tue, 14 May 2002 16:33:05 +0200 From: Andrea Bernini Subject: evaluation residence time of water To: chemistry@ccl.net Message-id: <001f01c1fb54$426feaa0$1c01a8c0@zeus> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 X-Mailer: Microsoft Outlook Express 5.00.2919.6700 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal Dear CCLers, I'm interested in evaluating the residence time of water molecules on protein surface through nanosecond-scale MD. While evaluating the RMSD of each water molecule along the dynamics trajectory is straightforward, I've not found any software implementing the statistical functions needed to evaluate residence times. Is anyone aware of a program capable of such evaluation or of an algorithm easy to be implemented? Thanks in advance, Andrea. ______________________________________________ Andrea Bernini, D. Phil. Molecular Biology Dept. University of Siena Via Fiorentina 1, 53100 Siena, Italy From chemistry-request@server.ccl.net Tue May 14 10:45:29 2002 Received: from mail-d.bcc.ac.uk ([144.82.100.24]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4EEjTg06526 for ; Tue, 14 May 2002 10:45:29 -0400 Received: from pop-c.ucl.ac.uk by mail-d.bcc.ac.uk with SMTP (Mailer) with ESMTP; Tue, 14 May 2002 15:45:27 +0100 Received: from socrates-a.ucl.ac.uk (socrates-a.ucl.ac.uk [144.82.100.160]) by pop-c.ucl.ac.uk (8.10.2+Sun/8.10.2) with ESMTP id g4EEiue29244; Tue, 14 May 2002 15:44:56 +0100 (BST) Date: Tue, 14 May 2002 15:44:55 +0100 (BST) From: Graeme Day To: dck cc: chemistry Subject: Re: CCL:how to suppress the standard orientation in G98? In-Reply-To: <3CE11953.B11E62F5@chemie.uni-dortmund.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-UCL-MailScanner: Found to be clean the keyword 'nosymm' will keep the atoms in their input orientation. Graeme On Tue, 14 May 2002, dck wrote: > hello! > > how can i suppress the standard orientation in G98, and force g98 to > calculate the molecules properties in the geometry, given in the input? > or in other words, what's the keyword or iop corresponding to the > coord=unique in GAMESS. > > yours > > dc kleb > > > -= 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 Tue May 14 11:29:42 2002 Received: from oc30.uni-paderborn.de ([131.234.240.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4EFTgg07445 for ; Tue, 14 May 2002 11:29:42 -0400 Received: (from ib@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) id VAA21484; Tue, 14 May 2002 21:02:52 +0200 (CEST) Date: Tue, 14 May 2002 21:02:52 +0200 (CEST) Message-Id: <200205141902.VAA21484@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: kleb@chemie.uni-dortmund.de CC: chemistry@ccl.net In-reply-to: <3CE11953.B11E62F5@chemie.uni-dortmund.de> (message from dck on Tue, 14 May 2002 16:04:03 +0200) Subject: Re: CCL:how to suppress the standard orientation in G98? References: <3CE11953.B11E62F5@chemie.uni-dortmund.de> Short answer, try NoSymm. Regards, Ingo Brunberg > Date: Tue, 14 May 2002 16:04:03 +0200 > From: dck > X-Accept-Language: de,en > Content-Type: text/plain; charset=us-ascii > Sender: "Computational Chemistry List" > Precedence: bulk > > hello! > > how can i suppress the standard orientation in G98, and force g98 to > calculate the molecules properties in the geometry, given in the input? > or in other words, what's the keyword or iop corresponding to the > coord=unique in GAMESS. > > yours > > dc kleb > From chemistry-request@server.ccl.net Tue May 14 12:41:03 2002 Received: from mxout3.cac.washington.edu ([140.142.32.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4EGf3g09486 for ; Tue, 14 May 2002 12:41:03 -0400 Received: from mailscan-out1.cac.washington.edu (mailscan-out1.cac.washington.edu [140.142.32.17]) by mxout3.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g4EGf2tr003300 for ; Tue, 14 May 2002 09:41:02 -0700 Received: FROM hymn04.u.washington.edu BY mailscan-out1.cac.washington.edu ; Tue May 14 09:41:02 2002 -0700 Received: from localhost (localhost [127.0.0.1]) by hymn04.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with ESMTP id g4EGf1vW010032 for ; Tue, 14 May 2002 09:41:01 -0700 Date: Tue, 14 May 2002 09:41:01 -0700 (PDT) From: Yu Chen To: chemistry@ccl.net Subject: Solvation Parameters for DNA In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Hi, I am looking for atomic solvation parameters for nucleic acid in CHARMM force field. Does anybody have any information about it? Thanks in advance, Yu Chen Department of Chemistry University of Washington, Seattle From chemistry-request@server.ccl.net Tue May 14 17:59:46 2002 Received: from mail-b.bcc.ac.uk ([144.82.100.22]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4ELxkg14608 for ; Tue, 14 May 2002 17:59:46 -0400 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Tue, 14 May 2002 22:59:31 +0100 Received: (from uccatvm@localhost) by socrates-a.ucl.ac.uk (8.11.6+Sun/8.9.3) id g4ELxUC29583; Tue, 14 May 2002 22:59:30 +0100 (BST) From: uccatvm Message-Id: <200205142159.g4ELxUC29583@socrates-a.ucl.ac.uk> Subject: Re: CCL:counterpoise with LMP2 To: chemistry@ccl.net (CCL) Date: Tue, 14 May 2002 22:59:30 +0100 (BST) Cc: T.vanMourik@ucl.ac.uk (Tanja van Mourik) In-Reply-To: <200205141228.g4ECSER02301@localhost.localdomain> from "Gerd Raether" at May 14, 2002 02:28:14 PM X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Gerd, Thank you for your answer. However, my question was more specifically how to get the best orbital domain match for the dimer and monomer+ghost calculations in local MP2, and not so much how to do counterpoise calculations in general. The SCF-MI methods of Mayer and co-workers are a different approach to deal with BSSE, and are not without problems. For example, with SCF-MI/VB method and the aug-cc-pV5Z basis set, the De of He2 is 10.64 K at 5.8 bohr - J. Mol. Struct. (Theochem) 549, 77, 2001. The FCI/aug-cc-pV5Z estimate is 10.17 K at 5.6 a.u. (J. Chem. Phys. 111, 9248, 1999). I think this shows that SCF-MI overestimates the interaction energy. Tanja > > maybe the work of Istvan Mayer et al. > > author = {I. Mayer and \'A. Vib\'ok and G. Hal\'asz and P. Valiron}, > title = {A BSSE-Free SCF Algorithm for Intermolecular > Interactions. III. Generarlization for Three-Body > Systems and for Using Bond Functions}, > journal = {Int. J. Quantum Chem.}, > year = {1996}, > volume = {57}, > pages = {1049} > > (see also the references there) is useful for you. This approach is > especially useful if you are going to use small basis sets. Here you > also get a BSSE free wave function. Furthermore as far as I know you > will find also a discussion how the classical Boys Bernardi Method > should be applied - this should be sufficient if you just go for BSSE > free energies. > > Gerd > > From: uccatvm > Date: Mon, 13 May 2002 21:56:43 +0100 (BST) > > Hi all, > > I am wondering what the most correct way is to do counterpoise with local > MP2. In the local MP2 method originally proposed by Pulay (Chem.Phys.Lett. > 100, 151, 1983), to each localised MO a subset (orbital domain) of the > virtual orbitals is assigned. To calculate the interaction energy of a > weakly interacting system, the orbital domains of the subsystems are first > determined at large distance, and used in subsequent dimer calculations at > smaller intermolecular distances (as recommended in for example Schutz et al., > J. Phys. Chem. 102, 5997, 1998). > > Now, I assume that (to keep a true counterpoise) it is best to use the > orbital domains determined at large distance for the monomer+ghost > calculation. For this, one would first have to determine the domains of the > monomer+ghost with the ghost at large R, and use the thus obtained orbital > domains in the monomer+ghost calculation at the smaller distance. What > do people think? Would this be the correct way of doing it? > > Of course, the BSSE is strongly reduced in LMP2, and should in principle > be negligible when using an appropriate basis set. However, when using > small basis sets it may not be negligible, and I would like to know the > best way of doing counterpoise for these cases. > > Thanks in advance, > > Tanja > > -- > ===================================================================== > Tanja van Mourik > Royal Society University Research Fellow > Chemistry Department > University College London phone: +44 (0)20-7679-4663 > 20 Gordon Street e-mail: work: T.vanMourik@ucl.ac.uk > London WC1H 0AJ, UK home: tanja@netcomuk.co.uk > > http://www.chem.ucl.ac.uk/people/vanmourik/index.html > ===================================================================== > > -= 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 Tue May 14 20:04:44 2002 Received: from web14601.mail.yahoo.com ([216.136.224.79]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4F04hg18182 for ; Tue, 14 May 2002 20:04:44 -0400 Message-ID: <20020515000442.35293.qmail@web14601.mail.yahoo.com> Received: from [61.9.73.249] by web14601.mail.yahoo.com via HTTP; Wed, 15 May 2002 01:04:42 BST Date: Wed, 15 May 2002 01:04:42 +0100 (BST) From: =?iso-8859-1?q?amor=20san=20juan?= Subject: Digested replies: Ligand preparation for AutoDock To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit CLLers: > > Do you know a freeware used in ligand preparation that > is capable of adding charge & implicit Hydrogens > exported as mol2 Sybyl file built in one package > program? > > Please let me know.Thanks in advance. > > Amor > UP-Diliman > Philippines > Dear Amor, ArgusLab is not free, but very inexpensive for academics. It can do what you want. If you are interested, you can download a trial copy at www.arguslab.com Mark Thompson Amor- I believe babel has a flag you must set in order for it to generate the gasteiger partial charges. try "-charge" on the babel command line. Geoff Hello, I´ve had the same problem. Have you tried Vega? It is free and available at http://users.unimi.it/~ddl/. It can convert a number of file formats (mol, mol2, pdb) and lists PDBQ explicitly as an output format. You can assign GASTEIGER charges by the switch -c GASTEIGER. Hope this helps, Christoph Nimptsch ------------------------------------------------- Christoph Nimptsch Apotheker Pharmazeutisches Institut Arbeitskreis Prof. Kovar Universität Tübingen Auf der Morgenstelle 8 D-72076 Tuebingen Tel.: 07071/2978794 mailto:christoph.nimptsch@uni-tuebingen.de ------------------------------------------------- Dear Amor We don't know exactly if AutoDock uses a proper file format (and if yes can you send us an example) but if your problem is solely convert from mol2 to pdbq (maybe assigning the partial charges) you can try our program VEGA http://users.unimi.it/~ddl that is able to make all these conversion and much more Best regards 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 ---------------------- Thanks for all the help extended fully. Cheers to all the AutoDocker's community. Amor San Juan University of the Philippines-Diliman __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From chemistry-request@server.ccl.net Tue May 14 11:13:36 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 g4EFDZg07106 for ; Tue, 14 May 2002 11:13:36 -0400 Received: from wrzx34.rz.uni-wuerzburg.de (wrzx34.rz.uni-wuerzburg.de [132.187.3.34]) by wrzx35.rz.uni-wuerzburg.de (8.8.8/8.8.8/uniwue-MM-1.04) with ESMTP id RAA29238 for ; Tue, 14 May 2002 17:13:34 +0200 (MET DST) Received: from localhost (localhost [127.0.0.1]) by wrzx34.rz.uni-wuerzburg.de (Postfix) with ESMTP id 8CF3EEE6 for ; Tue, 14 May 2002 17:13:34 +0200 (CEST) Received: from wrzx07.rz.uni-wuerzburg.de (wrzx07.rz.uni-wuerzburg.de [132.187.1.7]) by wrzx34.rz.uni-wuerzburg.de (Postfix) with ESMTP id 717C9D2D for ; Tue, 14 May 2002 17:13:34 +0200 (CEST) Received: from wocx51.chemie.uni-wuerzburg.de (wocx51.chemie.uni-wuerzburg.de [132.187.64.51]) by wrzx07.rz.uni-wuerzburg.de (Postfix) with ESMTP id 58E6B182 for ; Tue, 14 May 2002 17:13:34 +0200 (CEST) Received: from chemie.uni-wuerzburg.de (bernd@wocd70.chemie.uni-wuerzburg.de [132.187.64.170]) by wocx51.chemie.uni-wuerzburg.de (SGI-8.9.3/8.9.3/uniwue-M-1.0) with ESMTP id RAA69091 for ; Tue, 14 May 2002 17:13:34 +0200 (MESZ) Sender: bernd@chemie.uni-wuerzburg.de Message-ID: <3CE129C7.DA7C12D1@chemie.uni-wuerzburg.de> Date: Tue, 14 May 2002 17:14:15 +0200 From: Bernd Engels Organization: Institut =?iso-8859-1?Q?f=FCr?= Organische Chemie X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.10 i586) X-Accept-Language: en MIME-Version: 1.0 To: ccl Subject: conference announcement Content-Type: multipart/mixed; boundary="------------F3BFBEB76D80508F751A4BC4" X-Virus-Scanned: by AMaViS (Rechenzentrum Universitaet Wuerzburg) This is a multi-part message in MIME format. --------------F3BFBEB76D80508F751A4BC4 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCl's, Please find herewith the announcement of Conference on the highly interdisciplinary topic of electron density with all its implications in chemistry and physics. The conference takes place at the University of Würzburg from October 8 till 10, 2002. PLEASE VISIT OUR WEBSITE FOR MORE INFORMATION ON THE CONFERENCE: http://www-organik.chemie.uni-wuerzburg.de/gk_dicht/conference.htm Best regards, Bernd Engels -- Institut für Organische Chemie, Universität Würzburg Am Hubland 97074 Würzburg Germany Phone : (0049) (0)931-888-5394 Fax : (0049) (0)931-888-4606 e-mail: bernd@chemie.uni-wuerzburg.de --------------F3BFBEB76D80508F751A4BC4 Content-Type: text/x-vcard; charset=us-ascii; name="bernd.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Bernd Engels Content-Disposition: attachment; filename="bernd.vcf" begin:vcard n:Engels;Bernd tel;fax:0049-(0)931-888-4606 tel;work:0049-(0)931-888-5394 x-mozilla-html:FALSE org:Institut für Organische Chemie;der Universität Würzburg adr:;;;97074 Würzburg;Am Hubland;; version:2.1 email;internet:bernd@chemie.uni-wuerzburg.de x-mozilla-cpt:;9056 fn:Prof. Dr. Bernd Engels end:vcard --------------F3BFBEB76D80508F751A4BC4-- From chemistry-request@server.ccl.net Tue May 14 19:20:21 2002 Received: from gate-sl1.mdli.com ([208.200.221.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4ENKLg16888 for ; Tue, 14 May 2002 19:20:21 -0400 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id QAA20197; Tue, 14 May 2002 16:18:44 -0700 (PDT) Received: from puffin.mdli.com(172.16.1.12) by gate-sl1 via smap (V2.1) id xma020194; Tue, 14 May 02 16:18:39 -0700 Received: from exch-sl02.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id QAA76102; Tue, 14 May 2002 16:18:38 -0700 (PDT) Received: by exch-sl02.mdli.com with Internet Mail Service (5.5.2653.19) id ; Tue, 14 May 2002 16:18:38 -0700 Message-ID: From: Bob Snyder To: "'List Server, CHMINF'" , "'List Server, CCL'" , "'List Server, ACSMEDI'" , "'List Server, MOL-DIVERSITY'" Cc: Bob Snyder Subject: CINF Final Program for Boston 2002 Date: Tue, 14 May 2002 16:18:36 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain To aid the planning of your attendance at the Fall ACS meeting, here is the full program for the Division of Chemical Information (CINF). See you in Boston! Bob Snyder CINF Program Chair +++++++++++++++++++++++++++++++++++++++ DIVISION OF CHEMICAL INFORMATION (CINF) Final Program, 224th ACS National Meeting Boston, MA, August 18-22, 2002 Robert W. Snyder, Program Chair SUNDAY MORNING Section A Virtual High-Throughput Screening: Fast docking and Scoring O. F. Guner, Organizer M. Waldman, Presiding 9:00 - 1. Ultra High Throughput Screening using THINK on the Internet. E. K. Davies, C. J. Davies 9:30 - 2. Next steps for virtual screening and massively distributed computing. D. M. Potts 10:00 - 3. Evaluating protein-ligand interactions through flexible docking. T. Hurst 10:30 - 4. Docking of diverse ligands to diverse protein sites: six degrees of application. T. A. Lyons, M. Dooley, A. Lamy, S. Patel, R. Hoffmann, H. Bertrand, M. Lim-Wilby 11:00 - 5. eHiTS: Novel algorithm for fast, exhaustive flexible ligand docking and scoring Z. Zsoldos, A. P. Johnson, A. Simon, I. Szabo, Z. Szabo 11:30 - 6. Effect of electrostatic models on the accuracy of ligand docking. P. W. Payne Section B Integrated Access to Chemical and Other Data Sources K. A. Harrington, Organizer, Presiding 9:00 - 7. Integration Continuum...different strokes for different folks K. Schwall, E. M. Shanbrom 9:30 - 8. Hindsight is an exact science. J. N. Potter, C. Hardy, R. D. Brown, J. Hayward 10:00 - 9. Bridging the gap between published and proprietary spectroscopic databases: an informatics system case study. G. M. Banik, T. Abshear 10:30 - 10. Developing value-added organic chemistry databases from traditional print products. D. Henderson, C. Finley 11:00 - 11. Linking reaction information from different sources. G. Grethe, P. Loew, H. Kraut, J. Eiblmaier SUNDAY AFTERNOON Section A Virtual High-Throughput Screening: Property-based screening O. F. Guner, Organizer M. Waldman, Presiding 2:00 - 12. Reoptimization of MDL keys for use in drug discovery. K. T. Taylor, J. L. Durant Jr., B. A. Leland, D. R. Henry, J. G. Nourse 2:30 - 13. Strategies for Lead Discovery Oriented Virtual Screening. T. I. Oprea 3:00 - 14. Application of pharmacophore fingerprint keys to structure-based design and data mining. M. Waldman, M. Hassan, C. Lin, S. N. Rao, C. M. Venkatachalam 3:30 - 15. Quasi2: Virtual site model derivation and application to lead identification. D. G. Lloyd, N. C. Perry, N. P. Todorov, I. J. P. de Esch, I. L. Alberts 4:00 - 16. Identification of Potent and Novel ?4?1 Antagonists using In Silico Screening. J. Singh, S. Adams, W. Lee, H. van Vlijmen 4:30 - 17. Unified virtual ADME/Tox using a hierarchy of machine learning models. G. Lanza, W. Mydlowec 5:00 - 18. Application of 1D-similarity analysis to predict plausible modes of CYP-450 metabolism. C. Duraiswami, S. L. Dixon, J. J. Baldwin Section B Integrated Access to Chemical and Other Data Sources K. A. Harrington, Organizer, Presiding 2:00 - 19. Exact chemical structure batch mode searches. C. A. Lipinski 2:30 - 20. Integration of disparate data sources from genomics to chemistry. R. D. Brown, D. Benham 3:00 - 21. How to build and deploy chemoinformatics applications. L. J. Culot Jr. 3:30 - 22. Hybrid methodologies for pKa prediction and database selection. M. J. Rice, R. T. Weekley, W. K. Ridgeway, P. A. Sprengeler MONDAY MORNING Section A Virtual High-Throughput Screening: Novel Approches O. F. Guner, Organizer, Presiding 8:30 - 23. Rule-based two-layer model for virtual high throughput screening. R. M. Flaig, T. F. Kochmann, R. Eils 9:00 - 24. DNA decompiler for the establishment of bootstrapping rules. T. F. Kochmann, R. M. Flaig, C. Busold, R. Eils 9:30 - 25. Application of chemometric and QSAR approaches to scoring ligand-receptor binding affinity. A. Tropsha, J. Feng, A. Golbraikh, C. Breneman, W. Deng, N. Sukumar 10:00 - 26. Evaluation of ligand-receptor binding affinity with a novel statistical scoring function derived from Delaunay tessellation of protein-ligand interface. A. Tropsha, J. Feng 10:30 - 27. Massive Virtual Library (MVL) Screening at Biogen: An Integrated Approach From Medicinal Chemistry Design to Decision. D. N. Chin, C. Chuaqui, H. van Vlijmen, X. Zhang, R. Petter, J. Singh 11:00 - 28. Fuzzy logic based focused libraries (FL/FL) for HTS screening: application to anti-carcinogenic compounds. J. R. Chretien, M. Pintore, N. Piclin, F. Ros 11:30 - 29. Moore's Law and the future of virtual screening. W. Mydlowec Section B Digital Archiving C. Huber, Organizer, Presiding 8:30 - Introductory Remarks. 8:35 - 30. 100 years Houben-Weyl Methods of Organic Chemistry: Entering the New Millennium. G. F. Herrmann, R. Hoppe, K. Kurz 9:00 - 31. Building digital archives for scientific information. L. R. Solla 9:25 - 32. Digital Archiving: Experiences of a major commercial publishing house. C. A. Spiteri 9:50 - 33. DSpace: MIT's Digital Repository. M. Branschofsky 10:15 - 34. Implementing the Physical Review Online Archive (PROLA). M. D. Doyle 10:40 - 35. Journey from books to analytical informatics. M. Scandone, D. Kernan 11:05 - 36. LOCKSS: Lots of copies keeps stuff safe. V. Reich, G. Baysinger 11:30 - 37. Combining heterogeneous physical property data sets. P. J. Linstrom 11:55 - Discussion. MONDAY AFTERNOON Section A Virtual High-Throughput Screening: Advances in Software Tools O. F. Guner, Organizer, Presiding 2:00 - 38. Evaluation, Comparison and Successful Application of Virtual Screening Tools R. T. Kroemer, J. McDonald, D. Rohrer, A. Vulpetti, J. Trosset, S. Rao, J. Irwin, B. Shoichet, C. McMartin, P. Stouten 2:30 - 39. Assessing the quality of virtual screening results for combinatorial libraries. D. G. Sprous, R. D. Clark, J. M. Leonard, T. W. Heritage 3:00 - 40. Virtual high throughput screening using LigandFit as an accurate and very fast tool for docking, scoring, and ranking M. Lim-Wilby, J. Jiang, M. Waldman, C. M. Venkatachalam 3:30 - 41. EasyDock: a new docking program for high-throughput screening and binding-mode search. N. P. Todorov, R. L. Mancera, P. Kallblad, P. Monthoux 4:00 - 42. Glide: a new paradigm for rapid, accurate docking and scoring in database screening T. A. Halgren, R. B. Murphy, J. Banks, D. Mainz, J. Klicic, J. K. Perry, R. A. Friesner 4:30 - 43. RACHEL: A new tool for structure-based lead optimization. C. M. W. Ho 5:00 - 44. HostDesigner: a program for the de novo structure-based design of molecular receptors with binding sites that complement metal ion guests. T. K. Firman, B. P. Hay Section B Electronic Notebooks and Related Systems for Knowledge Management in R&D - State of the Technology R. Lysakowski Jr., Organizer 1:00 - 45. Collaborative eR&D - what is it and how do electronic notebooks fit into it ? R. Lysakowski Jr. 1:30 - 46. Components of Research Laboratory Notebooks Policy. S. C. Diaz 2:00 - 47. An E-Notebook success story, a roadmap for future trips C. J. Ruggles, J. Rizzi, J. Manrique 2:30 - 48. LabBook incorporated's eLabBook knowledge management solution. T. Tom Zupancic 3:00 - 49. Roundtable discussion focused on implementation successes and issues for collaborative electronic notebooks and collaborative eR&D environments. R. Lysakowski Jr. 3:30 - Intermission. 4:00 - 50. CINF Division Business Meeting. A. Berks 4:30 - 51. Open Meeting: Committees on Publications and on Chemical Abstracts Service. R. J. Massie, R. D. Bovenschulte MONDAY EVENING Sci-Mix R. W. Snyder, Organizer 8:00 PM - 10:00 PM 52. Development of a polymer property database from traditional print products. M. Johnson, D. Henderson 53. Teaching and learning of strucural organic chemistry with nomenclature/structure software. B. Ramsay, A. J. Williams, A. Erin, R. Martin 54. Homogenizing analytical data from multiple vendors into a unified workspace. A. J. Williams 55. Aventis Competitor Tracking Database. C. Rudolph, H. Heitsch, R. Munoz-Sanz 56. Knowledge management in the spectral laboratory. M. Scandone, G. M. Banik 57. Molecular docking for generating peptides inhibitors for thrombin. C. C. Clement, J. Gingold, M. Philipp 58. Visualization of results in markush structure database searches. A. H. Berks TUESDAY MORNING Skolnik Award Symposium: Searching and Indexing of Chemical Patents - Yesterday, Today, & Tomorrow G. Cross, Organizer P. Norton, Presiding 9:00 - Introductory Remarks. 9:05 - 59. Digging Deeper: from holes in cards to whole structures - indexing chemistry at Derwent. P. Norton 9:35 - 60. Polymer searching: a capability in progress. S. M. Kaback 10:05 - 61. Polymer indexing by IFI - past, present, and future H. M. Allcock, D. Slaughter 10:35 - 62. Broadening horizons, sharpening the focus: The challenges of searching multiple datasets to obtain focused recall R. W. Neale, S. Hajkowski, L. Clark, G. Cross TUESDAY AFTERNOON Skolnik Award Symposium: Searching and Indexing of Chemical Patents - Yesterday, Today, & Tomorrow G. Cross, Organizer P. Norton, Presiding 2:00 - Introductory Remarks. 2:05 - 63. Chemical patent indexing and Gresham's Law. E. S. Simmons 2:35 - 64. Chemical structures and reactions in CAS databases - searching for prior art. M. J. Toussant 3:05 - 65. Biotechnology patent searching: past, present and future S. Burcham 3:35 - 66. Back for the future: making coding cool. G. Cross, K. Hancox 4:05 - Concluding Remarks. WEDNESDAY MORNING Section A Combinatorial Chemistry Informatics P. Kocis, Organizer D. A. Evans, Organizer, Presiding 9:00 - 67. Developing HT Information Systems, a modular design S. Coles 9:30 - 68. Automating Library Design. M. J. Duffield, K. Daniels 10:00 - 69. On a new model for cheminformatics: Learning the classes of compounds. D. Korkin 10:30 - 70. Choosing the proper grid resolution for cell-based diversity estimation. D. N. Rassokhin, D. K. Agrafiotis 11:00 - 71. Quantification of drug-likeness and similarity for combinatorial follow-on libraries. M. J. Rice, R. T. Weekley, P. A. Sprengeler 11:30 - 72. Predicting generic methods and retention times for high-throughput chromatography. D. Jouravleva, S. Macdonald, M. McBrien, E. Kolovanov Section B Scientific Communications Today: Chemistry and Copyrights J. Rumble Jr., Organizer 9:00 - 73. Copyright and the EU Database Directive: Issues for chemistry. J. R. Rumble Jr. 9:30 - 74. Pressures on the public domain in scientific data and information. P. F. Uhlir 10:00 - 75. IPR and modern scientific society publishing. E. S. Slater 10:30 - 76. Copyright and the information industry. D. Duncan 11:00 - 77. Database protection and academic research. H. J. Onsrud 11:30 - 78. An academic chemist looks at copyright. S. S. Zimmerman WEDNESDAY AFTERNOON Section A Combinatorial Chemistry Informatics D. A. Evans, Organizer P. Kocis, Organizer, Presiding 2:00 - 79. Integration of Combinatorial Chemistry Analyses with Other Relevant Information. J. Saffer 2:30 - 80. Barriers to effective integration in chemical experiment management software. J. C. Phelan 3:00 - 81. Application of statistical design tools for improved efficiency in chemistry development for high-throughput parallel synthesis. J. E. Patterson, R. Nicewonger 3:30 - 82. Library design using multi-dimensional SAR analysis: Incorporating structure-based predictions. C. Sage, K. Holme, M. Sud 4:00 - 83. Use of recursive partitioning/simulated annealing (RP/SA) for mining combinatorial libraries. P. Blower, P. Kocis 4:30 - 84. NMR Prediction Software and Applications to the Screening of Combinatorial Libraries. A. J. Williams, S. Golotvin Section B Data Warehousing P. Caduff, Organizer 2:00 - 85. Computational proteomics: Genome-scale analysis of protein structure, function, & evolution M. Gerstein, P. Harrison, J. Qian, R. Jansen, V. Alexandrov, P. Bertone, R. Das, D. Greenbaum, W. Krebs, Y. Liu, H. Hegyi, N. Echols, J. Lin, C. Wilson, A. Drawid, Z. Zhang, Y. Kluger, N. Lan, N. Luscombe, S. Balasubramanian 2:30 - 86. Federated databases: The next level. P. M. Smith 3:00 - 87. Practical meta data solutions for the large data warehouse. T. Gransee, P. Vosters, R. Duncan 3:30 - 88. So you have a data warehouse - Now What? W. Langton, R. Durvasula, J. Pitney 4:00 - 89. Using OLAP and data mining technologies for trending, knowledge discovery, and collaborative commerce J. Griffin 4:30 - Panel Discussion. THURSDAY MORNING Section A Managing Genomic Information R. V. Buckley, Organizer 9:00 - Introductory Remarks. 9:05 - 90. Challenges of information provision in a dynamic genomic landscape. R. V. Buckley, G. Stokes 9:35 - 91. Integration of genomic, biological, and chemical data in drug discovery T. Laz 10:05 - 92. Genomics gorilla....handling sequence overload D. B. French, D. B. Sidhu, E. M. Shanbrom 10:35 - 93. Managing and providing biosequence information in the STN host environment. I. Schindler, R. Stuike-Prill 11:05 - 94. Multiscale hierarchical classifications of genes for genomics HTS analysis. C. Yang, L. Yu 11:35 - 95. Management, integration and cross-referencing of genomic information A. Caruso 12:05 - Concluding Remarks. Section B Careers in Chemical Information P. Barnett, Organizer 9:00 - 96. Life after the lab (or how to never leave university). P. E. Meindl 9:30 - 97. What to expect in a small corporate R&D library. S. C. Boito 10:00 - 98. Chemical information careers in the government. J. R. Rumble Jr. 10:30 - 99. Searching Patents: Background, careers and the future R. Kaminecki 11:00 - 100. Creating content and selling it: a career in publishing. K. Kurz 11:30 - 101. Some novel perspectives with a computational chemistry degree. J. L. Nauss THURSDAY AFTERNOON Use of Chemical Information R. W. Snyder, Organizer 1:00 - 102. Teaching and learning of strucural organic chemistry with nomenclature/structure software. B. Ramsay, A. J. Williams, A. Erin, R. Martin 1:30 - 103. Application integration: Providing coherent drug discovery solutions. M. Miller, M. Sud 2:00 - 104. The APRILSTM (Automated Plate Re-Mapping and Integrated Library Services) System: Using Open Source Tools to Solve Thorny Informatics Problems Inexpensively. M. R. Frierson III, B. Lou, S. Beltz 2:30 - 105. Homogenizing analytical data from multiple vendors into a unified workspace. A. J. Williams 3:00 - 106. Effective chemical information. J. M. Goodman 3:30 - 107. Snapshot of content, retrieval, and quality of some chemical information systems D. Rehm 4:00 - 108. Battling the data avalanche - a chemical data management solution for the smallcap company. K. K. Turnbull 4:30 - 109. Command and control of the drug discovery factory: Putting chemists in the driver's seat. D. Hadfield ------------------------------------- Robert W. Snyder, Ph.D. Director Database Marketing MDL Information Systems email: bobs@mdl.com telephone: +1-510-357-2222, ext. 1162 cell phone: +1-510-816-5112 text msg: 5108165112@mobile.att.net Never stop searching.