From chemistry-request@server.ccl.net Thu Nov 21 14:35:23 2002 Received: from TheWorld.com ([199.172.62.106]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gALJZN713531 for ; Thu, 21 Nov 2002 14:35:23 -0500 Received: from world.std.com (greywolf@world-f.std.com [199.172.62.5]) by TheWorld.com (8.9.3/8.9.3) with ESMTP id OAA03906 for ; Thu, 21 Nov 2002 14:35:23 -0500 Received: (from jle@localhost) by world.std.com (8.9.3/8.9.3) id OAA05298 for chemistry@ccl.net; Thu, 21 Nov 2002 14:35:11 -0500 (EST) Date: Thu, 21 Nov 2002 14:35:11 -0500 (EST) From: Joe M Leonard Message-Id: <200211211935.OAA05298@world.std.com> To: chemistry@ccl.net Subject: What are the MMFF94 atom types for Norastemizole? Folks, If anybody has Macromodel and/or Schrodinger products, could they please let me know the MMFF94 atom types for this molecule (particularly the 5-membered ring)? There does not seem to be a similar molecule in the validation suite... This is in reference to JMC 45, 3844(2002), Cavalli et al (structure #32). The smiles string (assuming I'm cutting/pasting correctly :-) is Fc4ccc(Cn3c(NC1CCNCC1)nc2ccccc23)cc4 Thanks in advance! Joe From chemistry-request@server.ccl.net Thu Nov 21 23:45:34 2002 Received: from fort-point-station.mit.edu ([18.7.7.76]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAM4jY731324 for ; Thu, 21 Nov 2002 23:45:34 -0500 Received: from grand-central-station.mit.edu (GRAND-CENTRAL-STATION.MIT.EDU [18.7.21.82]) by fort-point-station.mit.edu (8.9.2/8.9.2) with ESMTP id XAA24233 for ; Thu, 21 Nov 2002 23:45:33 -0500 (EST) Received: from melbourne-city-street.mit.edu (MELBOURNE-CITY-STREET.MIT.EDU [18.7.21.86]) by grand-central-station.mit.edu (8.9.2/8.9.2) with ESMTP id XAA26287 for ; Thu, 21 Nov 2002 23:45:33 -0500 (EST) Received: from buzzword-bingo.mit.edu (BUZZWORD-BINGO.MIT.EDU [18.7.16.73]) by melbourne-city-street.mit.edu (8.9.2/8.9.2) with ESMTP id XAA20039 for ; Thu, 21 Nov 2002 23:45:32 -0500 (EST) Received: from localhost (damians@localhost) by buzzword-bingo.mit.edu (8.9.3) with ESMTP id XAA16096; Thu, 21 Nov 2002 23:45:32 -0500 (EST) Date: Thu, 21 Nov 2002 23:45:32 -0500 (EST) From: Damian A Scherlis Perel To: Subject: Hartree-Fock and spin contamination Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, let me ask your opinion on how to interpret the following: I have done some calculations on a dimer formed by two radicals. It is known that in the dimer the unpaired electrons couple and the system becomes a singlet; GGA as well as B3LYP show agreement with this fact. However, in the case of Hartree-Fock calculations (using Gaussian 98), the triplet turns out to be significantly more stable -as much as 40 kcal/mol lower in energy-, but with a value for S**2 of about 4, which becomes twice that number after annihilation. By the way, let me add that the binding energies for this spin contaminated triplet are quite close to the B3LYP ones. On the other hand, the binding energies for the singlet dimer are unreasonably low if compared with B3LYP or GGA. I'd appreciate any suggestions about how to interpret these results. Is Gaussian converging to an excited singlet? If that is the case, is there a way to force convergence to the lowest state? I am in particular concerned about HF as a previous step to MP2. Lot of thanks. ------------------------ Damian Scherlis Department of Materials Science & Engineering Massachusetts Institute of Technology damians@mit.edu 617 253 6026 From chemistry-request@server.ccl.net Thu Nov 21 20:08:22 2002 Received: from smtp02.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAM18K728754 for ; Thu, 21 Nov 2002 20:08:21 -0500 Received: from lq (unknown [202.127.145.3]) by smtp02.sohu.com (Postfix) with ESMTP id AA9C06B89F for ; Fri, 22 Nov 2002 09:08:16 +0800 (CST) From: "=?GB2312?Q?=CB=AE=BF=CD?=" To: "CHEMISTRY@ccl.net" Subject: Where to get qcpe_ms for DOCK4 ? X-mailer: Foxmail 4.2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Date: Thu, 22 Nov 2001 9:8:2 +0800 Message-Id: <20021122010816.AA9C06B89F@smtp02.sohu.com> Dear DOCK4 Users, I'm a new user of DOCK4. By using it, I found that the program qcpe_ms is indispensable for the molecular surface calculation. And a molecular surface file is needed when running the sphgen. But qcpe_ms is not distributed with DOCK4. At least, I can not find it in the version which I got. And it is rather expensive to obtain the MS from QCPE. Now, will you please tell me, whether it is possible to get qcpe_ms freely, which is needed by the DOCK4 (in shell script autoMS). If possible, where and how could I got it? If you have other methods to generate the .ms for running the sphgen, please tell me! Thank you in advance for your help. Have a nice day!!! Yours Sincerely Li Qiang Shanghai Institute of Organic Chemistry Chinese Academy of Sciences No.354 Road FengLin ShangHai, 200032, China Phone: 08621-64163300-2735 From chemistry-request@server.ccl.net Fri Nov 22 03:26:25 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAM8QP704854 for ; Fri, 22 Nov 2002 03:26:25 -0500 Received: from CONVERSION-DAEMON.unisi.it by unisi.it (PMDF V6.0-025 #30546) id <01KP5WEM2H28000JB1@unisi.it> for chemistry@ccl.net; Fri, 22 Nov 2002 09:26:14 +0100 (MET) Received: from cuces.unisi.it (iris.ctf.unisi.it [172.16.3.79]) by unisi.it (PMDF V6.0-025 #30546) with ESMTPA id <01KP5WEK8DPY000JC0@unisi.it> for chemistry@ccl.net; Fri, 22 Nov 2002 09:26:03 +0100 (MET) Date: Fri, 22 Nov 2002 09:18:18 -0800 From: "Dr. Fabrizio Manetti" Subject: Fourth European Workshop in Drug Design (4EWDD) Sender: fabrizio@unisi.it To: chemistry@ccl.net Message-id: <3DDE66DA.CE6F9EBB@cuces.unisi.it> MIME-version: 1.0 X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) Content-type: multipart/mixed; boundary="Boundary_(ID_FQUs8XPdO/rQALgZn+8cPA)" X-Accept-Language: en This is a multi-part message in MIME format. --Boundary_(ID_FQUs8XPdO/rQALgZn+8cPA) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT --Boundary_(ID_FQUs8XPdO/rQALgZn+8cPA) Content-type: text/html; name=Lettera4EWDD; charset=us-ascii Content-transfer-encoding: 7BIT Content-disposition: inline; filename=Lettera4EWDD

The University of Siena is pleased to announce the

Fourth European Workshop in Drug Design


to be held in Certosa di  Pontignano (Siena), Italy, from

May 25 - June 01, 2003.

This workshop, which follows up the three very successful previous editions,
held respectively in Cortona on May 1995,
and in Siena on May 1998 and June 2001,
will feature about 20 well known researchers from the University
and the Pharmaceutical Industry, including directors of research,
working with a maximum number of 45 workshop participants.

Participants will be divided into teams, each team led by a tutor,
and will focus on solving concrete problems in drug design
using high level hardware and software tools,
including 20 workstations and a server contributed by SGI.

Talks and case studies will be interdisciplinary, touching upon
ligand/structure based drug design,
in silico ADME,
design and screening of virtual libraries,
molecular modelling methodologies,
molecular biology and synthetic feasibility, etc.
 

Participation in the Fourth European Workshop in Drug Design is limited to
  45 applicants, selected on the basis of individual experience.

Deadline for receiving applications,
fee for participation, web page address, etc.,
will be available in about a week and provided by a second circular.
 

On behalf of the Local Organizing Committee,
Dr. Fabrizio Manetti
Dipartimento Farmaco Chimico Tecnologico
Università degli Studi di Siena
Via Aldo Moro
I-53100 Siena, Italy
Phone: ++39 0577 234306
Fax:   ++39 0577 234333
Email: manettif@unisi.it

--Boundary_(ID_FQUs8XPdO/rQALgZn+8cPA)-- From chemistry-request@server.ccl.net Fri Nov 22 05:43:09 2002 Received: from nomina.net.lu.se ([130.235.132.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAMAh9707262 for ; Fri, 22 Nov 2002 05:43:09 -0500 Received: from csxp (CS-XP1800.mig.lu.se [130.235.104.90]) by nomina.net.lu.se (8.9.3/8.9.0) with SMTP id LAA17699 for ; Fri, 22 Nov 2002 11:43:37 +0100 (MET) Message-ID: <003901c29214$5ef1eeb0$5a68eb82@csxp> From: =?iso-8859-1?Q?Emanuel_Bj=F6rne?= To: Subject: Equilbrium constants? Date: Fri, 22 Nov 2002 11:46:10 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0036_01C2921C.C099CE00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0036_01C2921C.C099CE00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, Does anyone know a good source for equilbrium constants of known = protein/ligand complexes? Regards, Emanuel ------=_NextPart_000_0036_01C2921C.C099CE00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,
 
Does anyone know a good source for = equilbrium=20 constants of known protein/ligand complexes?
 
Regards,
 
Emanuel
------=_NextPart_000_0036_01C2921C.C099CE00-- From chemistry-request@server.ccl.net Fri Nov 22 03:55:21 2002 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAM8tL705414 for ; Fri, 22 Nov 2002 03:55:21 -0500 Received: from as2100.itodys.jussieu.fr (as2100.itodys.jussieu.fr [134.157.24.23]) by shiva.jussieu.fr (8.12.5/jtpda-5.4) with SMTP id gAM8tLjR015312 for ; Fri, 22 Nov 2002 09:55:21 +0100 (CET) Date: Fri, 22 Nov 2002 09:55:20 +0100 Message-Id: <02112209552056@itodys.jussieu.fr> From: petitjean@itodys.jussieu.fr To: chemistry@ccl.net Subject: CCL:freewares for modeling X-VMS-To: SMTP%"chemistry@ccl.net" X-Antivirus: scanned by sophie at shiva.jussieu.fr To: chemistry@ccl.net subj: CCL:freewares for modeling Dear CCL, I have build some freewares: ARMS: Spatial Alignment with the RMS (Root Mean Square) method. (protein backbones oriented; computes the common 3D motif after alignment)) ASV: Analytical calculation of van der Waals surfaces and volumes (Monte-Carlo included) CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules (works on any couple of 3D molecule; correspondence is computed) DOG: Docking Geometrically two molecules. POP: Optimal partitionning (works either on signed similarities or on categorical variables) (this is clustering rather than modeling) QCM: Qantitative Chirality Measure of a conformer (graph automorphisms included) documentation and download from: http://petitjeanmichel.free.fr/itoweb.petitjean.html RADI: Computation of the Radius and Diameter of a spatial set (convex hull, minimal sphere, geometric shape coefficient (D-R)/R, ...) To get documentation and/or binaries, just email me. (platforms: sgi, linux, compaq, and some others) Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean@ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 From chemistry-request@server.ccl.net Fri Nov 22 08:08:55 2002 Received: from dobit2.rug.ac.be ([157.193.42.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAMD8s709856 for ; Fri, 22 Nov 2002 08:08:55 -0500 Received: from allserv.rug.ac.be (allserv.rug.ac.be [157.193.40.42]) by dobit2.rug.ac.be (8.11.1/8.11.1) with ESMTP id gAMD8se10343 for ; Fri, 22 Nov 2002 14:08:54 +0100 (MET) Received: from hartree4.rug.ac.be (hartree4.rug.ac.be [157.193.91.12]) by allserv.rug.ac.be (8.11.1/8.11.1) with ESMTP id gAMD8rQ24111 for ; Fri, 22 Nov 2002 14:08:53 +0100 (MET) Received: from inchem34 (inchem34.rug.ac.be [157.193.91.54]) by hartree4.rug.ac.be (AIX4.2/UCB 8.7/8.7) with SMTP id PAA05370 for ; Fri, 22 Nov 2002 15:11:03 +0100 (NFT) Message-Id: <4.1.20021122135914.02aac950@127.0.0.1> X-Sender: patrick@157.193.91.12 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Fri, 22 Nov 2002 14:11:52 +0100 To: chemistry@ccl.net From: Patrick Bultinck Subject: How good are non variational methods ? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Antivirus: Avast32 (VPS 5/11/2002), Outbound message X-Antivirus-Status: Clean Dear all, I am curious in your ideas about what good non variational methods are in quantum chemistry ? In variational techniques (e.g. Hartree-Fock, CI) on minimizes the variational integral and through the variation theorem you know you will almost stay just above or equal to the true solution (at least for the energy). With e.g. perturbation theory, you may end up anywhere, that is: above, below or on the dot of the true solution. What is your opinion on techniques such as Coupled Cluster (iterative but in most formulations not variational, although I naively think this must be possible), or MP2, MP4, ... ? We often see "highly accurate" results of say CCSD(T) (using perturbation theory on top of the iterative scheme), but how to put this in perspective knowing that there is no variational theorem applicable ? Has this ever been discussed throughly in some reference ? What are the experiences of the CCL members ? Thanks for your ideas/time, Patrick Bultinck Quantum Chemistry Group Ghent University Belgium From chemistry-request@server.ccl.net Fri Nov 22 09:28:06 2002 Received: from srvus010.unitedcatalysts.com ([208.23.162.8]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gAMES6711564 for ; Fri, 22 Nov 2002 09:28:06 -0500 Received: by lvlxch02.unitedcatalysts.com with Internet Mail Service (5.5.2653.19) id ; Fri, 22 Nov 2002 09:27:40 -0500 Message-ID: <5CF08BBFE6DE97478C1E76E654CAF90822104E@lvlxch02.unitedcatalysts.com> From: "Shobe, Dave" To: "'Patrick Bultinck'" , "'CCL'" Subject: RE: How good are non variational methods ? Date: Fri, 22 Nov 2002 09:27:31 -0500 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 gAMES6711565 The example of CCSD(T) shows that nonvariational methods can have high accuracy. It seems to me that in the past few decades, quantum chemical methods developers have valued size consistency over variational-ness (I forget what the actual word is). After all if the method is not size-consistent, how can we trust it for dimerizations, dissociation energies, or any other reaction where groups of atoms come together or apart? And apparently it's difficult to find a level of theory other than HF and Full CI which is both size-consistent and variational. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Patrick Bultinck [mailto:Patrick.Bultinck@rug.ac.be] Sent: Friday, November 22, 2002 8:12 AM To: chemistry@ccl.net Subject: CCL:How good are non variational methods ? Dear all, I am curious in your ideas about what good non variational methods are in quantum chemistry ? In variational techniques (e.g. Hartree-Fock, CI) on minimizes the variational integral and through the variation theorem you know you will almost stay just above or equal to the true solution (at least for the energy). With e.g. perturbation theory, you may end up anywhere, that is: above, below or on the dot of the true solution. What is your opinion on techniques such as Coupled Cluster (iterative but in most formulations not variational, although I naively think this must be possible), or MP2, MP4, ... ? We often see "highly accurate" results of say CCSD(T) (using perturbation theory on top of the iterative scheme), but how to put this in perspective knowing that there is no variational theorem applicable ? Has this ever been discussed throughly in some reference ? What are the experiences of the CCL members ? Thanks for your ideas/time, Patrick Bultinck Quantum Chemistry Group Ghent University Belgium -= 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 Fri Nov 22 08:01:26 2002 Received: from guppy.vub.ac.be ([134.184.129.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAMD1P709753 for ; Fri, 22 Nov 2002 08:01:25 -0500 Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.3]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.1.ap (guppy)) id OAA03462; Fri, 22 Nov 2002 14:01:20 +0100 (MET) for From: cbiot@ulb.ac.be Received: from ulb.ac.be (chimorg-pc5.ulb.ac.be [164.15.61.104]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id OAA23549; Fri, 22 Nov 2002 14:01:17 +0100 (MET) for Message-ID: <3DDE3991.1000005@ulb.ac.be> Date: Fri, 22 Nov 2002 14:05:05 +0000 Organization: ULB User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: Liste CCL Subject: polar hydrogen Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear all, I'm searching for a program which can add polar hydrogens to pdb files. May I use a program like Babel and then remove the nonpolar hydrogens or should I use a program like "pol_h". Is it a free or share software? And if yes, Can you tell me how to download it? Best C Biot From chemistry-request@server.ccl.net Fri Nov 22 09:36:04 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 gAMEa3711855 for ; Fri, 22 Nov 2002 09:36:03 -0500 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Fri, 22 Nov 2002 14:36:02 +0000 Received: (from uccatvm@localhost) by socrates-a.ucl.ac.uk (8.11.6+Sun/8.9.3) id gAMEa1q28876; Fri, 22 Nov 2002 14:36:02 GMT From: uccatvm Message-Id: <200211221436.gAMEa1q28876@socrates-a.ucl.ac.uk> Subject: Re: CCL:How good are non variational methods ? To: Patrick.Bultinck@rug.ac.be (Patrick Bultinck) Date: Fri, 22 Nov 2002 14:36:01 +0000 (GMT) Cc: chemistry@ccl.net In-Reply-To: <4.1.20021122135914.02aac950@127.0.0.1> from "Patrick Bultinck" at Nov 22, 2002 02:11:52 PM X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Patrick, > What is your opinion on techniques such as Coupled Cluster (iterative but > in most formulations not variational, although I naively think this must be > possible), or MP2, MP4, ... ? We often see "highly accurate" results of say > CCSD(T) (using perturbation theory on top of the iterative scheme), but how > to put this in perspective knowing that there is no variational theorem > applicable ? > > Has this ever been discussed throughly in some reference ? What are the > experiences of the CCL members ? Although it may be useful to know the sign of the error in the computed energy (as in the case of variational methods), what is more important is that the error is small. One possible problem of (less than full) CI methods, for example, is their lack of size-extensivity, which is a problem when calculating interaction energies. CCSD(T) and MPn are size-extensive methods. There of course have been many studies comparing the accuracy of the different methods. A good starting reference is: "A road map for the calculation of molecular binding energies," TH Dunning, Jr. J Chem Phys A 104, 9063 (2000), and the many "Benchmark calculations" papers published by Dunning and co-workers. There have been many recent publications discussing the (non-)convergence of the MPn perturbation series, see for example (the list is far from complete); - Olsen J, Christiansen O, Koch H, et al. J Chem Phys 105, 5082-5090 (1996) - T.H. Dunning, Jr. and KA Peterson, J Chem Phys 108, 4761-4771 (1998) - Halkier, H. Larsen, J. Olsen, P. Jorgensen J. Chem. Phys. 110, 7127 (1999) - M.L. Leiniger, W.D. Allen, H.F. Schaefer III, C.D. Sherrill, J. Chem. Phys. 112, 9213 (2000) Hope his helps, 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_van_mourik@btopenworld.com http://www.chem.ucl.ac.uk/people/vanmourik/index.html ===================================================================== From chemistry-request@server.ccl.net Fri Nov 22 08:05:00 2002 Received: from hotmail.com ([216.33.241.98]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAMD50709805 for ; Fri, 22 Nov 2002 08:05:00 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 22 Nov 2002 05:05:00 -0800 Received: from 192.132.225.130 by lw8fd.law8.hotmail.msn.com with HTTP; Fri, 22 Nov 2002 13:05:00 GMT X-Originating-IP: [192.132.225.130] From: "Rehana Begum" To: CHEMISTRY@ccl.net Subject: DOCKING Date: Fri, 22 Nov 2002 13:05:00 +0000 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 22 Nov 2002 13:05:00.0939 (UTC) FILETIME=[C3FE2DB0:01C29227]
Dear all,
I am new to the world of molecular modeling and I was wondering if any of you can help me to begin understanding it.
I am taking a course in the Topics of Bioinformatics and I have to do a project using the SYBYL software (Tripos Inc).  I was planning on using the DOCKING method to determine the interaction between the ligand and an inhibitor.  If any one has done anything similar, please give me a few pointers as to how to go about doing it. 
Thanks in advance.
--Rehana

Add photos to your messages with MSN 8. Get 2 months FREE*. From chemistry-request@server.ccl.net Fri Nov 22 09:41:54 2002 Received: from exchange.neokimia.com ([132.210.158.207]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAMEfr712018 for ; Fri, 22 Nov 2002 09:41:53 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 content-class: urn:content-classes:message Subject: RE: Conformational search, Alchemy 2000 vs MM3 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C29235.1CD66AB2" Date: Fri, 22 Nov 2002 09:40:33 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: RE: Conformational search, Alchemy 2000 vs MM3 Thread-Index: AcKSNVW4NJ1wGwzqR26mju+D0dlY4g== From: "Axel Mathieu" To: This is a multi-part message in MIME format. ------_=_NextPart_001_01C29235.1CD66AB2 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Yep, I had the same problem with similarly sized macrocyclic molecules. = Unfortunately, I've never used Alchemy - I use MOE. Through our = validation for the conformational analysis of our macrocyclic = moleculess, we discovered that the result is entirely forcefield = dependent. In other words, different forcefields gave a different amount = of conformers given identical conformational searches - which obviously = displayed different levels of reproducibility. In order to solve this, = we evaluated all the forcefields at our displosal at the time and = several confromational searches to find a reproducible, relatively short = conformational search resulting in a workable amonut of conformers. = Therefore, my suggestion is to do the same with your molecules = (especially if you have several differnt molecules of similar ring sizes = to verify). It takes a while, but it is worth it for future searches. = BTW, what kind of conformational search are you performing on your = macrocyclic molecule? =20 Axel =20 =20 -----Original Message----- From: Adel El-Azhary [mailto:azhary@ksu.edu.sa]=20 Sent: 21 novembre, 2002 07:54 To: chemistry@ccl.net Subject: CCL:Conformational search, Alchemy 2000 vs MM3 Deae CCL users: =20 I am doing conformational search using the Alchemy 2000 program. It = looks that my molecule has a large ring of 18 atoms and the number of = possible conformations is quite large and taking a quite lot of effort. = This is because I create say 200 conformations and then do MM3 geometry = optimization on each manually and then examine each output. I have to = repeat this step for about a 100 time. I was thinking that the MM3(2000) = program running on unix might be more firiendly. Does anyone has a = suggestion or a similar experience.=20 =20 Best regards, =20 Adel El-Azhary =20 Axel Mathieu, Ph.D. Computational Chemist/Mod=E9lisation Mol=E9culaire NEOKIMIA INC. Tel: (819) 820-6840 Fax: (819) 820-6841 www.neokimia.com =20 =20 =20 ------_=_NextPart_001_01C29235.1CD66AB2 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Message
Yep, I=20 had the same problem with similarly sized macrocyclic molecules. = Unfortunately,=20 I've never used Alchemy - I use MOE. Through our validation for the=20 conformational analysis of our macrocyclic moleculess, we discovered = that the=20 result is entirely forcefield dependent. In other words, different = forcefields=20 gave a different amount of conformers given identical conformational = searches -=20 which obviously displayed different levels of reproducibility. In order = to solve=20 this, we evaluated all the forcefields at our displosal at the time and = several=20 confromational searches to find a reproducible, relatively short = conformational=20 search resulting in a workable amonut of conformers. Therefore, my = suggestion is=20 to do the same with your molecules (especially if you have several = differnt=20 molecules of similar ring sizes to verify). It takes a while, but it is = worth it=20 for future searches. BTW, what kind of conformational search are you = performing=20 on your macrocyclic molecule?
 
Axel  
 
 -----Original = Message-----
From: Adel=20 El-Azhary [mailto:azhary@ksu.edu.sa]
Sent: 21 novembre, 2002=20 07:54
To: chemistry@ccl.net
Subject: = CCL:Conformational=20 search, Alchemy 2000 vs MM3

Deae CCL users:
 
I am doing conformational search using = the Alchemy=20 2000 program. It looks that my molecule has a large ring of 18 atoms and = the=20 number of possible conformations is quite large and taking a quite lot = of=20 effort. This is because I create say 200 conformations and then do MM3 = geometry=20 optimization on each manually and then examine each output. I have to = repeat=20 this step for about a 100 time. I was = thinking=20 that the MM3(2000) program running on unix might be more firiendly. Does = anyone=20 has a suggestion or a similar experience.
 
Best regards,
 
Adel = El-Azhary
 
Axel Mathieu, = Ph.D.
Computational Chemist/Mod=E9lisation=20 Mol=E9culaire
NEOKIMIA INC.
Tel: (819) 820-6840
Fax: (819) 820-6841
www.neokimia.com
 
 
------_=_NextPart_001_01C29235.1CD66AB2-- From chemistry-request@server.ccl.net Fri Nov 22 13:01:52 2002 Received: from sandmail01.sd.accelrys.com ([209.120.169.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAMI1p716818 for ; Fri, 22 Nov 2002 13:01:51 -0500 To: chminf-l@listserv.indiana.edu, chemistry@server.ccl.net Cc: qsar_society@accelrys.com Subject: CORRECTION - Deadline for submitting papers for ACS CINF program MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: From: osman@accelrys.com Date: Fri, 22 Nov 2002 10:01:47 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 11/22/2002 10:01:52 AM, Serialize complete at 11/22/2002 10:01:52 AM Content-Type: multipart/alternative; boundary="=_alternative 0062E47288256C79_=" This is a multipart message in MIME format. --=_alternative 0062E47288256C79_= Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable My apologies for submitting incorrect information and wasted bandwidth. The deadline for submitting abstracts for the CINF division is November=20 28th. The 22nd is the BTEC division deadline. Please use the following=20 link to enter the OASYS [http://oasys.acs.org/oasys.htm] and click on BTEC = for submitting papers to the Pharmacogenomics symposium (deadline today),=20 and click on the CINF for submitting papers for all the cheminformatics=20 sessions (deadline 28th). Again I apologize for the misinformation... looking forward to receiving=20 many intriguing submissions to the symposia. Thx...osman ----- Forwarded by Osman F Guner/San Diego/Accelrys on 11/22/2002 09:53 AM = ----- osman@accelrys.com Sent by: qsar=5Fsociety-admin@accelrys.com 11/21/2002 04:04 PM Please respond to qsar=5Fsociety =20 To: chminf-l@listserv.indiana.edu, chemistry@server.ccl.net cc: qsar=5Fsociety@accelrys.com Subject: QSAR - Deadline for submitting papers for ACS CINF = program is tomorrow the=20 22nd CINF=20 DIVISION OF CHEMICAL INFORMATION=20 The deadline for abstract submission is tomorrow the 22nd. There are=20 still some room for additional papers. Note that if you miss the deadline = but still interested in submitting a paper, please contact either myself=20 or the session chair directly, as it will be possible to enter your=20 abstract manually by early December.=20 Librarian watch: Introduction to new hot areas in chemistry=20 Cosponsored with Division of Chemical Education K. Porter and E. Kajosalo, Organizers=20 There is opening for up to four more papers... contact: kajosalo@mit.edu=20 and/or porter@library.vanderbilt.edu=20 Chemical Information Literacy -- is it affordable?=20 Cosponsored with Division of Chemical Education K. Porter and E. Kajosalo, Organizers=20 One more paper will close this session... contact: kajosalo@mit.edu and/or = porter@library.vanderbilt.edu Last Wave? Reference books go digital=20 E. Kajosalo, Organizer=20 One more paper will close this session... contact: kajosalo@mit.edu Michael O'Hara Memorial symposium=20 Cosponsored with PIUG, ACS Committee on Patents and Related Matters, and=20 Division of Chemistry and the Law A. H. Berks, Organizer=20 Can still take up to three more papers... contact: Andrew=5Fberks@merck.com= =20 High-throughput experimentation=20 Cosponsored with Division of Industrial and Engineering Chemistry L. A. Harmon, Organizer=20 Can still take up to three more papers... contact: lharmon@striatus.com=20 Patent Searching for Non-Expert A. H. Berks, Organizer=20 One more paper and this session is closed. Contact:=20 Andrew=5Fberks@merck.com=20 Posters O. F. G=FCner, Organizer=20 Keep'em coming... contact: osman@accelrys.com=20 Informatics Challenges in Toxicology and Environmental=20 Cosponsored with Division of Environmental Chemistry, and Division of=20 Chemical Toxicology S. Lee, Organizer=20 Two openings left. Contact: S.Lee@mdl.com=20 The scientific article in the digital world: where are we and where should = we be going? D. P. Martinsen, Organizer, Presiding=20 We can really use your help here... up to 5 more papers. Contact:=20 d=5Fmartinsen@acs.org=20 Knowledge Discovery and Scientific Numerical Databases J. Rumble Jr., Organizer=20 This one is full, but I'm sure we can squeeze in another paper. Contact:=20 John.rumble@nist.gov=20 Combinatorial chemistry and laboratory automation=20 Cosponsored with Division of Laboratory Automation D. A. Evans, Organizer=20 Opening for up to three more papers... Contact: davide@mdl.com=20 Current status of XML in chemistry=20 Cosponsored with CSA Trust B. A. Vickery, Organizer=20 One more paper, perhaps: Contact: bryan.vickery@chemweb.com=20 E-Commerce: What it is, and what it is not? T. Wright, Organizer=20 Opening for up to 4 papers, Contact: terryw@mdl.com=20 General Papers O. F. G=FCner, Organizer=20 Keep'em coming... osman@accelrys.com=20 Informatics challenges in pharmacogenomics=20 Cosponsored with Biotechnology Secretariat=20 This is listed under BTEC (not CINF) and can use up to 3 additional=20 speakers. The deadline for abstract submission for BTEC has passed so=20 please forward your abstracts directly to me at osman@accelrys.com=20 Osman F. G=FCner, Ph.D. Executive Director Cheminformatics and Rational Drug Design Accelrys Inc., 858-799-5341 osman@accelrys.com, http://www.accelrys.com --=_alternative 0062E47288256C79_= Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
My apologies for submitting incorrec= t information and wasted bandwidth.

The deadline for submitting abstract= s for the CINF division is November 28th.  The 22nd is the BTEC divisi= on deadline.  Please use the following link to enter the OASYS [http:/= /oasys.acs.org/oasys.htm] and click on BTEC for submitting papers to the Ph= armacogenomics symposium (deadline today), and click on the CINF for submit= ting papers for all the cheminformatics sessions (deadline 28th).

Again I apologize for the misinforma= tion... looking forward to receiving many intriguing submissions to the sym= posia.

Thx...osman

----- Forwarded by O= sman F Guner/San Diego/Accelrys on 11/22/2002 09:53 AM -----
osman@accelrys.com
Sent by: qsar=5Fsociety-admin@accelr= ys.com

11/21/2002 04:04 PM
Please respond to qsar=5Fsociety

       
        To: &nbs= p;      chminf-l@listserv.indiana.edu, chemistry@server.ccl.= net
        cc: &nbs= p;      qsar=5Fsociety@accelrys.com
        Subject:=        QSAR - Deadline for submitting papers for ACS C= INF program is tomorrow the 22nd




CINF

DIVISION OF CHEMICAL INFORMATION

The deadline for abstract submis= sion is tomorrow the 22nd.  There are still some room for additional p= apers.  Note that if you miss the deadline but still interested in sub= mitting a paper, please contact either myself or the session chair directly= , as it will be possible to enter your abstract manually by early December.=


Librarian watch: Introduction to new hot areas in chemistry
Cosponsored with Division of Chemical Education
K. Porter and E. Kajosalo, Organizers
There is opening for up to four more papers... contact: kajosalo@mit.edu an= d/or porter@library.vanderbilt.edu

Chemical Information Literacy -- is it affordable?
Cosponsored with Division of Chemical Education
K. Porter and E. Kajosalo, Organizers
One more paper will close this session... contact: kajosalo@mit.edu and/or = porter@library.vanderbilt.edu

Last Wave? Reference books go digital
E. Kajosalo, Organizer
One more paper will close this session... contact: kajosalo@mit.edu

Michael O'Hara Memorial symposium
Cosponsored with PIUG, ACS Committee on Patents and Related Matters, and Di= vision of Chemistry and the Law
A. H. Berks, Organizer
Can still take up to three more papers... contact: Andrew=5Fberks@merck.com=

High-throughput experimentation
Cosponsored with Division of Industrial and Engineering Chemistry
L. A. Harmon, Organizer
Can still take up to three more papers... contact: lharmon@striatus.com=

Patent Searching for Non-Expert
A. H. Berks, Organizer
One more paper and this session is closed.  Contact: Andrew=5Fberks@me= rck.com

Posters
O. F. G=FCner, Organizer
Keep'em coming... contact: osman@accelrys.com

Informatics Challenges in Toxicology and Environmental
Cosponsored with Division of Environmental Chemistry, and Division of Chemi= cal Toxicology
S. Lee, Organizer
Two openings left.  Contact: S.Lee@mdl.com

The scientific article in the digital world: where are we and where should = we be going?
D. P. Martinsen, Organizer, Presiding
We can really use your help here... up to 5 more papers.  Contact: d= =5Fmartinsen@acs.org

Knowledge Discovery and Scientific Numerical Databases
J. Rumble Jr., Organizer
This one is full, but I'm sure we can squeeze in another paper.  Conta= ct: John.rumble@nist.gov=

Combinatorial chemistry and laboratory automation
Cosponsored with Division of Laboratory Automation
D. A. Evans, Organizer
Opening for up to three more papers... Contact: davide@mdl.com

Current status of XML in chemistry
Cosponsored with CSA Trust
B. A. Vickery, Organizer
One more paper, perhaps:  Contact: bryan.vickery@chemweb.com

E-Commerce: What it is, and what it is not?
T. Wright, Organizer
Opening for up to 4 papers,  Contact: terryw@mdl.com

General Papers
O. F. G=FCner, Organizer
Keep'em coming... osman@accelrys.com

Informatics challenges in pharmacogenomics
Cosponsored with Biotechnology Secretariat
This is listed under BTEC (not CINF) and can use up to 3 additional speaker= s.  The deadline for abstract submission for BTEC has passed so please= forward your abstracts directly to me at osman@accelrys.com




Osman F. G=FCner, Ph.D.
Executive Director
Cheminformatics and Rational Drug Design
Accelrys Inc.,  858-799-5341
osman@accelrys.com, http://www.accelrys.com

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