From chemistry-request@server.ccl.net Thu Jan 16 23:45:23 2003 Received: from relay.nic.in ([164.100.10.106]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0H4jKV24679 for ; Thu, 16 Jan 2003 23:45:21 -0500 Received: from relay.nic.in (localhost [127.0.0.1]) by relay.nic.in (8.12.5/8.12.5) with ESMTP id h0H55s2c024500 for ; Fri, 17 Jan 2003 10:35:54 +0530 Received: from hau.nic.in (hau.nic.in [164.100.242.138]) by relay.nic.in (8.12.5/8.12.5) with ESMTP id h0H55ZZx024452 for ; Fri, 17 Jan 2003 10:35:44 +0530 Received: from dna (local.2.197 [192.168.2.197]) by hau.nic.in (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTPA id <0H8U0000GCRUGK@hau.nic.in> for chemistry@ccl.net; Fri, 17 Jan 2003 10:06:06 +0530 (IST) Date: Fri, 17 Jan 2003 10:03:44 +0530 From: "Dr. Sudhir Kumar" Subject: Installation of ADT on Windows/RedHat Linux To: "'Computational Chemistry List'" Message-id: <000701c2bde1$a1b01d00$c502a8c0@dna> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Mailer: Microsoft Outlook, Build 10.0.3416 Content-type: multipart/alternative; boundary="Boundary_(ID_spV0B2TJw0/yA+RLZbPQww)" Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal This is a multi-part message in MIME format. --Boundary_(ID_spV0B2TJw0/yA+RLZbPQww) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Dear CCLers, I am a new member of CCL and am a beginner in learning drug-design (particularly docking). I have downloaded ADT from MDL's site. What are pre-requisites of running ADT on a Windows (XP) machine? I have already installed Python2.0.1 but when run the INITADT.py or other scripts.. an error comes like: "Import error: No module named Numeric" what does this mean? How to compile/run ADT on a Linux machine (Redhat 7.1)? Thanks all _____________________________________________________ Dr. Sudhir Kumar Associate Professor Department of Chemistry CCS Haryana Agricultural University, Hisar - 125 004, INDIA http://hau.nic.in/sudhir.htm --Boundary_(ID_spV0B2TJw0/yA+RLZbPQww) Content-type: text/html; charset=us-ascii Content-transfer-encoding: 7BIT

Dear CCLers,

I am a new member of CCL and am a beginner in learning drug-design (particularly docking). I have downloaded ADT from MDL’s site.

What are pre-requisites of running ADT on a Windows (XP) machine? I have already installed Python2.0.1 but when run the INITADT.py or other scripts.. an error comes like:

“Import error: No module named Numeric”

what does this mean?

How to compile/run ADT on a Linux machine (Redhat 7.1)?

Thanks all

_____________________________________________________

Dr. Sudhir Kumar

Associate Professor

Department of Chemistry

CCS Haryana Agricultural University, Hisar - 125 004, INDIA

http://hau.nic.in/sudhir.htm

--Boundary_(ID_spV0B2TJw0/yA+RLZbPQww)-- From chemistry-request@server.ccl.net Fri Jan 17 07:18:54 2003 Received: from savo ([200.140.159.221]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h0HCIoV14470 for ; Fri, 17 Jan 2003 07:18:51 -0500 From: Bernadette Jablonski To: Subject: Far East Secrets to Longevity Date: Sat, 18 Jan 2003 04:24:51 -0800 Mime-Version: 1.0 Content-Type: text/html Message-Id: Hello, chemistry@ccl.net

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From chemistry-request@server.ccl.net Fri Jan 17 08:01:33 2003 Received: from neo.chemie.uni-erlangen.de ([131.188.128.233]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0HD1WV15173 for ; Fri, 17 Jan 2003 08:01:33 -0500 Received: by neo.chemie.uni-erlangen.de (Postfix, from userid 9145) id BDFCBBADD; Fri, 17 Jan 2003 14:09:47 +0100 (CET) Content-Type: text/plain; charset="iso-8859-15" From: olaf othersen Reply-To: olaf.othersen@chemie.uni-erlangen.de Organization: Computer Chemie Centrum To: CHEMISTRY@ccl.net Subject: TINKER TIP3P water in MM3-force field Date: Fri, 17 Jan 2003 14:09:47 +0100 User-Agent: KMail/1.4.3 MIME-Version: 1.0 Message-Id: <200301171409.47336.olaf.othersen@chemie.uni-erlangen.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h0HD1XV15174 Hi, I would like to use TINKER for the MD-simulation of a donor-acceptor-complex in water. I already have parametrized the donor-acceptor-complex and created the coordinates of a suitable water box. My problem are the parameters of TIP3P water adapted to the MM3 force field: I found no parameters for a fast water model in the mm3.prm - file, but there are TIP3P waters in other .prm-files The TINKER CHARMM force field seems to use similar Force Field Definition as MM3. The differences I found are: vdwtype LENNARD-JONES <=> MM3-HBOND dielectric 1.5 <=> 1.0 Is it possible to adapt the CHARMM-parameters for TIP3P water to MM3, or has anybody TIP3P parameters for water in the MM3-force field? I would appreciate your advice. Thank you in advance, Olaf Othersen Computational Chemistry Center Universität Erlangen-Nürnberg From chemistry-request@server.ccl.net Fri Jan 17 09:42:01 2003 Received: from iris ([152.66.63.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0HEg0V17945 for ; Fri, 17 Jan 2003 09:42:00 -0500 Received: from janka (helo=localhost) by iris with local-esmtp (Exim 3.35 #1 (Debian)) id 18ZXh2-0005L3-00 for ; Fri, 17 Jan 2003 15:42:00 +0100 Date: Fri, 17 Jan 2003 15:42:00 +0100 (CET) From: Matrai Janka To: CHEMISTRY@ccl.net Subject: HyperChem In-Reply-To: <200301171409.47336.olaf.othersen@chemie.uni-erlangen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I would like to ask some basic helps for the HyperChem conformational search option. I don't know how to define the torsion angles and in the manual we have got here there is no indication about it. If you have any experience please send me an answer, thanks a lot Janka From chemistry-request@server.ccl.net Fri Jan 17 10:23:34 2003 Received: from gip2.u-picardie.fr ([193.49.184.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0HFNXV18856 for ; Fri, 17 Jan 2003 10:23:34 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 71F7B9295; Fri, 17 Jan 2003 16:23:33 +0100 (CET) To: chemistry@ccl.net Subject: Shared memory & g98 Message-ID: <1042817013.3e281ff5653fe@webmail.u-picardie.fr> Date: Fri, 17 Jan 2003 16:23:33 +0100 (CET) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear All, I am trying to run g98 in parallel on a dual processor Alpha under Tru64/OSF1 using shared memory (i.e. not linda). Under Linux dual proc. we should use the following command: echo "Maximum_shared_memory_value_available" > /proc/sys/kernel/shmmax to increase the amount of shared memory. - What is the corresponding command under Alpha Tru64/OSF1 ? Indeed, the "file" /proc/sys/kernel/shmmax does not exist under Alpha Tru64/OSF1... - Same question under SGI IRIX ? Thanks, regards, Francois From chemistry-request@server.ccl.net Fri Jan 17 11:10:50 2003 Received: from mail-b.bcc.ac.uk ([144.82.100.22]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0HGAnV20104 for ; Fri, 17 Jan 2003 11:10:49 -0500 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Fri, 17 Jan 2003 16:10:48 +0000 Received: (from uccatvm@localhost) by socrates-a.ucl.ac.uk (8.11.6+Sun/8.9.3) id h0HGAld13440; Fri, 17 Jan 2003 16:10:47 GMT From: uccatvm Message-Id: <200301171610.h0HGAld13440@socrates-a.ucl.ac.uk> Subject: Re: CCL:Shared memory & g98 To: fyd@u-picardie.fr (FyD) Date: Fri, 17 Jan 2003 16:10:47 +0000 (GMT) Cc: chemistry@ccl.net In-Reply-To: <1042817013.3e281ff5653fe@webmail.u-picardie.fr> from "FyD" at Jan 17, 2003 04:23:33 PM X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Francois, > > I am trying to run g98 in parallel on a dual processor Alpha under Tru64/OSF1 > using shared memory (i.e. not linda). Under Linux dual proc. we should use the > following command: > echo "Maximum_shared_memory_value_available" > /proc/sys/kernel/shmmax > to increase the amount of shared memory. > > - What is the corresponding command under Alpha Tru64/OSF1 ? > Indeed, the "file" /proc/sys/kernel/shmmax does not exist under Alpha > Tru64/OSF1... > > - Same question under SGI IRIX ? How to increase the size of the shared memory limit on different architectures can be found on the Global Arrays support page on the NWChem web page: (http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html), follow "Global Array Library", "support"). Hope that 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 Jan 17 12:43:09 2003 Received: from umbi3.umbi.umd.edu ([136.160.7.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0HHh8V22406 for ; Fri, 17 Jan 2003 12:43:09 -0500 Received: from umbi.umd.edu ([129.6.112.59]) by umbi3.umbi.umd.edu (Netscape Messaging Server 4.15) with SMTP id H8VDBN00.3B4 for ; Fri, 17 Jan 2003 12:45:23 -0500 Message-ID: <3E284335.3464C3D@umbi.umd.edu> Date: Fri, 17 Jan 2003 12:53:57 -0500 From: "Michael K. Gilson" Organization: CARB/UMBI X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: UPS for Linux cluster Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit We are building a Linux cluster and are looking into UPSs for the machines. It looks cheaper (per VA rating) to buy a lot of deskside UPSs, but this is a less elegant solution than buying a few high-capacity supplies. Is there any reason, other than cabling issues, not to use a larger number of the smaller deskside power supplies? Any recommendations for specific units (large or small) would be appreciated also! Thanks in advance, Mike Gilson From chemistry-request@server.ccl.net Fri Jan 17 13:27:18 2003 Received: from ns1.tudelft.nl ([130.161.180.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0HIRHV23170 for ; Fri, 17 Jan 2003 13:27:17 -0500 Received: from CONVERSION-DAEMON.mailhost2.tudelft.nl by mailhost2.tudelft.nl (PMDF V6.1-1 #40925) id <0H8V00001F9FHZ@mailhost2.tudelft.nl> for chemistry@ccl.net; Fri, 17 Jan 2003 19:27:17 +0100 (MET) Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost2.tudelft.nl (PMDF V6.1-1 #40925) with ESMTP id <0H8V00HI8F9FXH@mailhost2.tudelft.nl> for chemistry@ccl.net; Fri, 17 Jan 2003 19:27:15 +0100 (MET) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.12.5/8.12.5) with ESMTP id h0HIRFsA009135 for ; Fri, 17 Jan 2003 19:27:15 +0100 (MET) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Fri, 17 Jan 2003 19:27:14 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Fri, 17 Jan 2003 19:27:04 +0000 (MET-1MEST) Date: Fri, 17 Jan 2003 19:27:04 +0100 From: Martijn Zwijnenburg Subject: RDEDX gamess-uk To: chemistry@ccl.net Message-id: <3E2858E3.14609.BB3CA0BF@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Hi, I have a problem with gamess-uk. When I try to run a job containing 12 silicon en 24 oxygen atoms and a 6-311G* basis-set I get the following error message: Error detected invalid number of words in rdedx After which the job crashes. I'am I correct to assume that this is a memory problem? But wat puzzels me then is that just before it says: invalid no of words: requested, present= 132 607 Looks to me that there is more present then requested and that sounds good, at least to me. Does anybody has a solution to this problem except running it on more processors (I tried 4 processors via mpi on a beowulf cluster with 1Gb of memory each)? Cheers, Martijn P.S. With a 6-31G* basis the job run without any problems ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@server.ccl.net Fri Jan 17 10:52:42 2003 Received: from mx20b.rmci.net ([205.162.184.38]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h0HFqfV19727 for ; Fri, 17 Jan 2003 10:52:41 -0500 Received: (qmail 9297 invoked from network); 17 Jan 2003 15:52:41 -0000 Received: from webmailb.rmci.net (HELO velocitus.net) (205.162.184.93) by mx20.rmci.net with SMTP; 17 Jan 2003 15:52:41 -0000 Received: from 132.178.216.35 (SquirrelMail authenticated user lwarner@velocitus.net) by webmail.velocitus.net with HTTP; Fri, 17 Jan 2003 08:52:41 -0700 (MST) Message-ID: <1097.132.178.216.35.1042818761.squirrel@webmail.velocitus.net> Date: Fri, 17 Jan 2003 08:52:41 -0700 (MST) Subject: Re: CCL:Dissociation Constant From: To: In-Reply-To: References: X-Priority: 3 Importance: Normal X-MSMail-Priority: Normal Cc: X-Mailer: SquirrelMail (version 1.2.7) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit No databases that I am aware of, but PubMed is a good resource for journal articles that may be of help. http://www.ncbi.nlm.nih.gov/PubMed/ > Dear CCLers, > > I'm looking for Dissociation Constant (Kd) of protein-protein complex, > If anyone knows about a public database or publication that has this > information of as many complex as possible, I will really appreciate > it. > > Thanks in advance > > Javier Cuervo > Graduate student > Computational Sciences Program SDSU > > > > -= 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 Jan 17 09:39:36 2003 Received: from dsa.mpi-muelheim.mpg.de ([192.108.70.121]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0HEdZV17893 for ; Fri, 17 Jan 2003 09:39:35 -0500 Received: from pctritux ([172.17.104.6]) by dsa.mpi-muelheim.mpg.de (8.11.3/8.11.3) with ESMTP id h0HEdO3320713 for ; Fri, 17 Jan 2003 15:39:24 +0100 (MET) Content-Type: text/plain; charset="iso-8859-1" From: Rolf Trinoga Reply-To: trinoga@mpi-muelheim.mpg.de Organization: Max-Planck-Institut fuer Strahlenchemie Subject: g98 for Linux and a new LINDA problem Date: Fri, 17 Jan 2003 15:42:35 +0100 User-Agent: KMail/1.4.3 To: MIME-Version: 1.0 Message-Id: <200301171542.35317.trinoga@mpi-muelheim.mpg.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h0HEdaV17894 Dear netters: I have the following problem trying to make G98 run in paralell with LINDA: We have built a LINUX Clusters with 40 nodes. I have compiled G98 Rev A11 with Portland Compiler (V4.02) on Red Hat 8.0 (kernel 2.4.18-14) and it runs very good. We purchased Linda and get a tar file: linda62-rh7.tar After installing linda and mg linda I got several *.exel files in the g98 directory and a linda-exe directory with links to the *.exel files. Starting a parallel job with g98l stops with lib not found: [trinoga@icmaster ~]$ g98l x.com setenv GAUSS_EXEDIR /opt/g98/linda-exe:/opt/g98/bsd:/opt/g98/local:/opt/g98/extras:/opt/g98 g98 x.com /opt/g98/linda-exe/l302.exel: error while loading shared libraries: util.so: cannot open shared object file: No such file or directory ntsnet: too many workers exited to continue ntsnet: needed: 1, started: 1, died: 1 ldd shows that the link tries to use /opt/g98/util.so [trinoga@icmaster ~]$ ldd /opt/g98/linda-exe/l302.exel util.so => /opt/g98/util.so (0x40013000) libm.so.6 => /lib/i686/libm.so.6 (0x43a2a000) libc.so.6 => /lib/i686/libc.so.6 (0x43a4c000) libpgc.so => /opt/pgi/linux86/lib/libpgc.so (0x43b7b000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) The lib util.so is in the right place and redable: [trinoga@icmaster ~]$ ls -l /opt/g98/util.so -rwxr-xr-x 1 trinoga stn 8691115 Dec 20 16:11 /opt/g98/util.so Is there anybody with an idea ??? -- Rolf Trinoga Max-Planck-Institut fuer Strahlenchemie Stiftstr. 34-36 D-45470 Muelheim a.d. Ruhr Germany Tel.: +49(208)306-3558 trinoga@mpi-muelheim.mpg.de http://www.mpi-muelheim.mpg.de/mpistr-home.html From chemistry-request@server.ccl.net Fri Jan 17 13:46:19 2003 Received: from kafka.net.nih.gov ([165.112.130.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0HIkJV23591 for ; Fri, 17 Jan 2003 13:46:19 -0500 Received: from I.T.S.ME ([129.43.27.170]) by kafka.net.nih.gov (/8.10.1) with ESMTP id h0HIkJsE007625; Fri, 17 Jan 2003 13:46:19 -0500 (EST) Date: Fri, 17 Jan 2003 13:45:04 -0500 (Eastern Standard Time) From: "M. Nicklaus" To: CHEMISTRY@ccl.net cc: mn1@helix.nih.gov Subject: Solution Structure Databases Message-ID: X-X-Sender: mn1@helix.nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know of a database, preferably publicly/freely accessible, of solution conformations of small molecules? I guess these would typically be NMR-determined structures. Solvent of primary interest would of course be water; but other solvents might be of interest, too. This wouldn't have to be a multi-hundred-thousand compound database. Still, of course, the larger the better. Any useful answers will be summarized. Thanks is advance, Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick E-mail: mn1@helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design MiniCore Facility Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Jan 17 15:44:09 2003 Received: from viper.abbott.com ([130.36.44.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0HKi9V25937 for ; Fri, 17 Jan 2003 15:44:09 -0500 Received: from abtmr1.abbott.com (abtmr1.abbott.com [10.254.245.1]) by viper.abbott.com (Switch-2.1.4/Switch-2.1.0) with ESMTP id h0HKiFp13782; Fri, 17 Jan 2003 14:44:15 -0600 (CST) Received: from abtapn561.northamerica.intra.abbott.com (localhost [127.0.0.1]) by abtmr1.abbott.com (Switch-2.0.6/Switch-2.0.6) with ESMTP id h0HKi8k11402; Fri, 17 Jan 2003 14:44:08 -0600 (CST) To: jcuervo@sciences.sdsu.edu, chemistry@ccl.net Cc: james.metz@abbott.com Subject: CCL: protein-protein dissociation constant X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Message-ID: From: james.metz@abbott.com Date: Fri, 17 Jan 2003 14:43:19 -0600 X-MIMETrack: Serialize by Router on ABTAPN561/ESVR/ABBOTT(Release 5.0.5 |September 22, 2000) at 01/17/2003 02:39:52 PM, Serialize complete at 01/17/2003 02:39:52 PM MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_alternative 0071E6E086256CB1_=" This is a multipart message in MIME format. --=_alternative 0071E6E086256CB1_= Content-Type: text/plain; charset="us-ascii" Javier, I am not aware of any databases of protein-protein dissociation constants either. First, take a look at the article, Horton, N. and Lewis, M. Protein Sci (1992) 1, 169, which describes the development of a semi-empirical, fast method to calculate Kd's for protein - protein complexes based on atomic solvation parameters, accessible surface areas, etc. I think there were a decent number of experimentally determined Kd's listed somewhere in the paper. Second, not to self-promote, but you might also want to get a copy of my Ph.D. thesis (Purdue Univ., Chem. Dept, 1991). In collaboration with Eli Lillly and Company, I used AMBER FEP methodology to calculate the relative self-association free energies of several insulin analogues using various thermodynamic cycles involving insulin monomers and dimers. I never published this work, because I couldn't get the relative numbers to tightly agree with experiment, but I did correctly predict the trends in self-association for 5 different insulin complexes. The Ph.D. thesis does contain a table or two with experimentally determined Kd data from analytical ultracentrifugation measurements. Third, you might want to consider the program PLOGP from the Institute of Physical Chemistry, Peking (contact Gao Ying at gao@mdl.ipc.pku.edu.cn). Primary literature reference is : Tao, P et al. J. Mol. Model. (1999) 5, 189. This very interesting program calculates logP values for peptides and even entire proteins, and you can visualize the molecular lipophilicity as a contour map, etc. Regards, Jim Metz James T. Metz, Ph.D. Research Investigator Chemist GPRD R46Y AP10-2 Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-6100 U.S.A. Office (847) 936 - 0441 FAX (847) 935 - 0548 james.metz@abbott.com --=_alternative 0071E6E086256CB1_= Content-Type: text/html; charset="us-ascii"
Javier,

I am not aware of any databases of protein-protein dissociation constants either.

First, take a look at the article, Horton, N. and Lewis, M. Protein Sci (1992) 1, 169, which describes the development of a semi-empirical, fast method to calculate Kd's for protein - protein complexes based on atomic solvation parameters, accessible surface areas, etc. I think there were a decent number of experimentally determined Kd's listed somewhere in the paper.

Second, not to self-promote, but you might also want to get a copy of my Ph.D. thesis (Purdue Univ., Chem. Dept, 1991). In collaboration with Eli Lillly and Company, I used AMBER FEP methodology to calculate the relative self-association free energies of several insulin analogues using various thermodynamic cycles involving insulin monomers and dimers. I never published this work, because I couldn't get the relative numbers to tightly agree with experiment, but I did correctly predict the trends in self-association for 5 different insulin complexes. The Ph.D. thesis does contain a table or two with experimentally determined Kd data from analytical ultracentrifugation measurements.

Third, you might want to consider the program PLOGP from the Institute of Physical Chemistry, Peking (contact Gao Ying at
gao@mdl.ipc.pku.edu.cn). Primary literature reference is : Tao, P et al. J. Mol. Model. (1999) 5, 189. This very interesting program calculates
logP values for peptides and even entire proteins, and you can visualize the molecular lipophilicity as a contour map, etc.

Regards,
Jim Metz

James T. Metz, Ph.D.
Research Investigator Chemist

GPRD R46Y AP10-2
Abbott Laboratories
100 Abbott Park Road
Abbott Park, IL 60064-6100
U.S.A.

Office (847) 936 - 0441
FAX (847) 935 - 0548

james.metz@abbott.com
--=_alternative 0071E6E086256CB1_=-- From chemistry-request@server.ccl.net Fri Jan 17 21:05:37 2003 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0I25aV30903 for ; Fri, 17 Jan 2003 21:05:37 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.6/TSRI-4.1rx) with SMTP id h0I25a800480 for ; Fri, 17 Jan 2003 18:05:36 -0800 (PST) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id 29782; Fri, 17 Jan 2003 17:59:48 -0800 (PST) Received: from gage.scripps.edu (gage.scripps.edu [137.131.252.115]) by relay1.scripps.edu (8.11.6/TSRI-4.2rAV) with ESMTP id h0I25VZ02069; Fri, 17 Jan 2003 18:05:31 -0800 (PST) Received: from gage (localhost [127.0.0.1]) by gage.scripps.edu (8.9.2/TSRI-3.0.1) with ESMTP id RAA02967; Fri, 17 Jan 2003 17:39:01 -0800 (PST) Message-Id: <200301180139.RAA02967@gage.scripps.edu> To: chemistry@ccl.net cc: bashford@scripps.edu, Vlad Cojocaru Subject: New version of MEAD released Date: Fri, 17 Jan 2003 17:39:00 -0800 From: Don Bashford Version 2.2.0p3 of MEAD is now available for anonymous FTP > from ftp.scripps.edu in directory /pub/electrostatics. MEAD is a suite of programs and software library that implements the model, Macroscopic Electricstatic with Atomic Detail (MEAD), thus the name. Applications inlude calculations of solvation energy, pKa calculations for proteins, etc. MEAD is relased as free software under the GNU General Public License. It should be possible to compile and run it on any Unix-like system with a standards-conforming C++ compiler. Changes from the previously released version, 2.2.0p2, are minor but necessary for compilation on more recent compilers, such as gcc-3.2 which is found on some of the latest GNU/Linux distributions (e.g. SuSe 8.1). Thanks to Vlad Cojocaru for bringing some of these problems to my attention. I believe he also posted about them to the list. The new release resolves the compilation problems he found. Have fun, Donald Bashford The Scripps Research Institute bashford@scripps.edu