From chemistry-request@server.ccl.net Mon Nov 1 05:10:01 1999 Received: from mail.iitk.ac.in (root@[210.212.54.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA24774 for ; Mon, 1 Nov 1999 05:09:57 -0500 Received: from qasid.cc.iitk.ernet.in (qasid.cc.iitk.ernet.in [172.31.1.16]) by mail.iitk.ac.in (8.9.3/8.9.3) with ESMTP id PAA03856 for ; Mon, 1 Nov 1999 15:36:13 +0530 Received: from mailer (IDENT:mary@mailer.cc.iitk.ernet.in [172.31.1.15]) by qasid.cc.iitk.ernet.in (8.9.1a/8.9.1) with ESMTP id PAA13707 for ; Mon, 1 Nov 1999 15:36:07 +0530 Date: Mon, 1 Nov 1999 15:32:34 +0530 (IST) From: "T.Meyarivan" X-Sender: mary@mailer.cc.iitk.ernet.in To: chemistry@ccl.net Subject: Genetic algorithms in chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, can someone enlighten me as to the extent of use of genetic algorithms in problem solving in chemistry. I have heard people use it for protein docking simulations, energy minimization calculations etc but since none of them make their code available its difficult to verify it. Since a vast majority of problem solving in chemistry using computers involves search , i feel that genetic algorithms would fit in nicely in such a application. with regards, T.Meyarivan From chemistry-request@server.ccl.net Mon Nov 1 05:45:29 1999 Received: from osi.lanet.lv (sgi.osi.lanet.lv [195.13.135.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA24938 for ; Mon, 1 Nov 1999 05:43:13 -0500 Received: from osi30.osi.lanet.lv (osi30.osi.lanet.lv [195.13.135.30]) by osi.lanet.lv (980427.SGI.8.8.8/8.8.8) with SMTP id MAA21277 for ; Mon, 1 Nov 1999 12:38:17 +0200 (EET) Message-Id: <1.5.4.32.19991101113954.0068d31c@sgi.osi.lanet.lv> X-Sender: misha@sgi.osi.lanet.lv X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 01 Nov 1999 13:39:54 +0200 To: chemistry@ccl.net From: Mendel Fleisher Subject: Mopac parameters Dear CCL`ers, I am looking for Na and K parameters for Mopac (AM1,PM3). Thanks in advance M.Fleisher ---------------------------------------------------------------- Dr. Mendel FLEISHER Phone +371-7-551822 Latvian Institute of Org.Synthesis FAX +371-7-821038 Aizkraukles str. 21 E-mail: misha@osi.lanet.lv LV-1006 Riga LATVIA Web: http://www.osi.lanet.lv ----------------------------------------------------------------- From chemistry-request@server.ccl.net Sun Oct 31 04:29:52 1999 Received: from linux2.ipc.pku.edu.cn (taop@linux2.ipc.pku.edu.cn [162.105.177.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA19263 for ; Sun, 31 Oct 1999 04:29:49 -0500 Received: from localhost (taop@localhost) by linux2.ipc.pku.edu.cn (8.8.7/8.8.7) with SMTP id RAA22344 for ; Sun, 31 Oct 1999 17:28:50 +0800 Date: Sun, 31 Oct 1999 17:28:50 +0800 (CST) From: Tao Peng To: CHEMISTRY@server.ccl.net Subject: Where to get qcpe_ms for DOCK4? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 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? Thank you in advance for your help. Have a nice day!!! Yours Sincerely Tao Peng \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\* \* Tao Peng \ \* \* Molecular Design Laboratory \ E-mail:taop@mdl.ipc.pku.edu.cn \* \* Institute of Physical Chemistry \ Lab Phone: 86-10-62756833 \* \* Peking University \ Fax Number:86-10-62751725 \* \* Beijing, 100871 \ http://linux2.ipc.pku.edu.cn/~taop \* \* P.R.China \ Dormitory Phone: 86-10-62761206 \* \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\* From chemistry-request@server.ccl.net Mon Nov 1 17:08:08 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA28826 for ; Mon, 1 Nov 1999 17:08:08 -0500 Received: from elvis.scripps.edu (elvis.scripps.edu [137.131.130.25]) by relay1.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id OAA25076; Mon, 1 Nov 1999 14:00:56 -0800 (PST) Received: from localhost (yadavm@localhost) by elvis.scripps.edu (8.9.2/TSRI-3.0) with SMTP id OAA177547; Mon, 1 Nov 1999 14:00:57 -0800 (PST) Date: Mon, 1 Nov 1999 14:00:57 -0800 (PST) From: Maneesh Yadav To: "T.Meyarivan" cc: chemistry@ccl.net Subject: Re: CCL:Genetic algorithms in chemistry In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi ! You may want to check out Autodock from Art Olson's group (www.scripps.edu then to research than to Art Olson than to Autodock), which uses GA's for searching conformation space; source is also available. THere really isn't much to look at except to know that the gene that they are using is a quaterinion and I'm not sure of what the mutation/crossover metrics are. Best of Luck MAneesh On Mon, 1 Nov 1999, T.Meyarivan wrote: > Hi, > can someone enlighten me as to the extent of use of genetic algorithms > in problem solving in chemistry. I have heard people use it for > protein docking simulations, energy minimization calculations etc > but since none of them make their code available its difficult to > verify it. Since a vast majority of problem solving in chemistry using > computers involves search , i feel that genetic algorithms would fit > in nicely in such a application. > > > with regards, > > T.Meyarivan > > > > -= 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 Mon Nov 1 14:52:11 1999 Received: from fer-net.fcq.unc.edu.ar (root@[200.16.18.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA27911 for ; Mon, 1 Nov 1999 14:47:50 -0500 Received: from fer-net.fcq.unc.edu.ar (IDENT:marcos@localhost [127.0.0.1]) by fer-net.fcq.unc.edu.ar (8.9.3/8.9.3) with SMTP id PAA14433 for ; Mon, 1 Nov 1999 15:52:00 -0500 From: Marcos Villarreal Organization: UNC, Dpto. Qca. Biol.-CIQUIBIC To: chemistry@ccl.net Subject: Parallel CHARMM Date: Mon, 1 Nov 1999 15:39:20 -0500 X-Mailer: KMail [version 1.0.17] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <99110115520000.14144@fer-net.fcq.unc.edu.ar> Content-Transfer-Encoding: 8bit Hello, I posted this question some time ago. By that time my mail server was down. So here it goes again. Could anybody please tell me how to COMPILE and RUN CHARMM c26b1 in a dual 266 Mhz PII with RH 6.0 and LAM-MPI (lam-6.3-b2-usysv)? Thanks in advance, Marcos ----------------------------------------------- PhD student Marcos Villarreal Departamento de Quimica Biologica Facultad de Ciencias Quimicas Universidad Nacional de Cordoba Argentina From chemistry-request@server.ccl.net Mon Nov 1 17:26:59 1999 Received: from mailbox1.ucsd.edu (mailbox1.ucsd.edu [132.239.1.53]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA28923 for ; Mon, 1 Nov 1999 17:26:59 -0500 Received: from chemcca10.ucsd.edu (chemcca10.ucsd.edu [132.239.156.10]) by mailbox1.ucsd.edu (8.9.3/8.9.3) with ESMTP id OAA24545 for <@mailbox.UCSD.EDU:chemistry@ccl.net>; Mon, 1 Nov 1999 14:22:04 -0800 (PST) Received: from chemcca10.ucsd.edu (chemcca19.ucsd.edu [132.239.156.49]) by chemcca10.ucsd.edu (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id OAA19977; Mon, 1 Nov 1999 14:22:03 -0800 (PST) Message-ID: <381EBB43.339DEC20@chemcca10.ucsd.edu> Date: Tue, 02 Nov 1999 02:21:55 -0800 From: "Heather A. Carlson" X-Mailer: Mozilla 4.51 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, hcarlson@chemcca10.ucsd.edu Subject: receptor flexibility in CADD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello All, We all know that it is a limitation to use a single protein structure to represent a target site on a protein. However, many of us still use that approach as there is no accepted way of accommodating the inherent flexibility of an active site in computer aided drug design. There are many means of accommodating ligand flexibility... I am interested in receptor flexibility. I've recently developed a method for superimposing multiple protein conformations to represent the inherent flexibility of a receptor when developing a complementary pharmacophore model (an ASAP article is available through J Phys Chem A: Carlson, Masukawa, McCammon). The only other work I have found that is at all similar is a ligand docking study by Knegtel, Kuntz, and Oshiro (J Mol Biol 1997, 266, 424-440) which introduces weighting methods either for the interaction energy between a ligand and the receptor or in the description the geometry of the site. Does anyone know of methods for accommodating an ensemble of protein conformations? Has anyone tried a similar idea without success or know of particularly interesting cases where the lack of protein flexibility leads to incorrect predictions? Thank you, Heather ___________________________________________________________________ Dr. Heather A. Carlson, Ph.D. American Cancer Society Postdoctoral Fellow La Jolla Interfaces in Science - BWF Postdoctoral Fellow UCSD, Dept. of Chemistry and Biochemistry Phone: (858) 822-1469 9500 Gilman Drive, 4202 Urey Hall Fax: (858) 534-7042 La Jolla, CA 92093-0365 E-mail: hcarlson@chemcca10.ucsd.edu ___________________________________________________________________ From chemistry-request@server.ccl.net Mon Nov 1 17:49:29 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA29155 for ; Mon, 1 Nov 1999 17:49:29 -0500 Received: from zosia (zosia.dorf.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-12 #D3869) with SMTP id <01JHUD0FWISM0006S8@mail.rwth-aachen.de> for chemistry@ccl.net; Tue, 2 Nov 1999 00:46:04 +0200 Date: Mon, 01 Nov 1999 23:43:30 +0100 From: Krzysztof Radacki Subject: bond order in G98 X-Sender: kradacki@mail.rwth-aachen.de To: chemistry@ccl.net Message-id: <3.0.6.32.19991101234330.007d9d70@mail.rwth-aachen.de> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Content-type: text/plain; charset="us-ascii" Hi CCL-ers, can somebody explain me how can I get covalent bond order from Gaussian? I've tried for two jobs that I want compare AIM=BondOrder. In one case I've got: THE MOLECULAR GRAPH IS DISCONNECTED ... ABORTING! in other: NEWTON STEP FAILED FOR SURFACE SHEET 1. The molecule are enough big that I don't want to calculate it per hand useing Density Matrix. regards Krzys Radacki ___________________---------------------------------------------------- ------------------ e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ----------------------------------------------------------------------