From chemistry-request@server.ccl.net Fri Mar 9 07:43:09 2001 Received: from web12305.mail.yahoo.com (web12305.mail.yahoo.com [216.136.173.103]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f29Ch8w09078 for ; Fri, 9 Mar 2001 07:43:09 -0500 Message-ID: <20010309124308.11095.qmail@web12305.mail.yahoo.com> Received: from [150.164.20.132] by web12305.mail.yahoo.com; Fri, 09 Mar 2001 09:43:08 ART Date: Fri, 9 Mar 2001 09:43:08 -0300 (ART) From: =?iso-8859-1?q?Tania=20Grigolli?= Subject: logP for windows To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi... I'm a brazilian graduate student, and I did the download of the xlogP program. I wrote to Gao Ying and he send me the crypt key. Thus, I asked him if there is some similar program for Windows version. He answerd me that he did not know and gave me your mail. Please, do you know if there is any free program like this but for Windows? I'm waiting for your answer, if it's possible... Thank you, so much ! sincerely Tânia ________________________________________________________________________ O YAHOO! GEOCITIES CHEGOU AO BRASIL! Crie sua home page com tudo em português - http://br.geocities.com From chemistry-request@server.ccl.net Fri Mar 9 08:24:56 2001 Received: from icod.ccti.ull.es (icod.ccti.ull.es [193.145.120.37]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f29DOuw09191 for ; Fri, 9 Mar 2001 08:24:56 -0500 Received: from ull.es (unknown [193.145.106.38]) by icod.ccti.ull.es (Postfix) with ESMTP id 2F46541A9 for ; Fri, 9 Mar 2001 13:24:55 +0000 (UCT) Message-ID: <3AA8D827.18330EAD@ull.es> Date: Fri, 09 Mar 2001 13:18:31 +0000 From: Pilar Carro Reply-To: pcarro@ull.es Organization: Dpto Quimica Fisica X-Mailer: Mozilla 4.5 [es] (Win98; I) X-Accept-Language: es MIME-Version: 1.0 To: chemistry@ccl.net Subject: SCIPCM for solvation of cluster Au10 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, I am trying to calculate the solvation of a cluster of 10 atoms of gold with G98W employing the IPCM method. My route section is: #P B3LYP/Gen Pseudo=Read SCF=tight Nosymm SCRF(SCIPCM) Before it begins L502 appear the following error message: A solvent integration origin lies outside the cavity! Would anybody know where is the problem? Thanks in advance for your help, P. Carro From chemistry-request@server.ccl.net Fri Mar 9 09:07:11 2001 Received: from oxmail.ox.ac.uk (oxmail4.ox.ac.uk [163.1.2.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f29E7Aw09443 for ; Fri, 9 Mar 2001 09:07:11 -0500 Received: from ermine.ox.ac.uk ([163.1.2.13]) by oxmail.ox.ac.uk with esmtp (Exim 3.12 #1) id 14bNXx-00047J-00 for chemistry@ccl.net; Fri, 09 Mar 2001 14:07:09 +0000 Received: from ivan (helo=localhost) by ermine.ox.ac.uk with local-esmtp (Exim 3.13 #1) id 14bNXx-0006J8-00 for chemistry@ccl.net; Fri, 09 Mar 2001 14:07:09 +0000 Date: Fri, 9 Mar 2001 14:07:09 +0000 (GMT) From: "Ivan I. Oleinik" To: chemistry@ccl.net Subject: DFT for astronomers Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I friend of mine who is astronomer asked me about review papers that can provide comprehensible introduction to density functional theory. Can anyone recommend the papers that would contain general overview of the theory and the field as well as discussion about capabilities, limitations, future opportunities for studying molecular and solid state systems? Thanks very much, Ivan Oleinik ------------------------------------------------------------------------ Ivan I. Oleinik E-mail : ivan.oleinik@materials.ox.ac.uk Department of Materials University of Oxford Parks Road Oxford OX1 3PH Tel : +44 (0)1865 283325 United Kingdom Fax : +44 (0)1865 273764 ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Mar 9 10:08:30 2001 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f29F8Uw09679 for ; Fri, 9 Mar 2001 10:08:30 -0500 Received: from vega (vega.farma.unimi.it [159.149.79.32]) by mailserver.unimi.it (8.9.3/8.9.3) with SMTP id QAA30391; Fri, 9 Mar 2001 16:08:21 +0100 (MET) Message-ID: <001401c0a8aa$bfa14da0$204f959f@farma.unimi.it.farma.unimi.it> From: "Giulio Vistoli" To: "Tania Grigolli" , References: <20010309124308.11095.qmail@web12305.mail.yahoo.com> Subject: Re: CCL:logP for windows Date: Fri, 9 Mar 2001 16:07:57 +0100 Organization: Ist. Chimica Farmaceutica Dear Tania, VEGA package is able to predict the logP according to Broto-Moreau and Ghose-Crippen methods (atomic fragments). Full VEGA version is also able to calculate the virtual logP according to Testa's MLP method and to build the MLP surface. VEGA can run in windows system and in UNIX system and a graphical version of this program for Win32 will be available as soon as possible. In order to download Vega software point your browser to http://users.unimi.it/~ddl P.S. To obtain the full version please contact us Best regards Giulio Vistoli -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39-02-29502230 Fax +39-02-29514197 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Fri Mar 9 10:57:51 2001 Received: from pegasus.arc.nasa.gov (pegasus.arc.nasa.gov [128.102.199.140]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f29Fvow09882 for ; Fri, 9 Mar 2001 10:57:50 -0500 Received: (from ricca@localhost) by pegasus.arc.nasa.gov (8.11.1/8.11.1) id f29FvX726495 for chemistry@ccl.net; Fri, 9 Mar 2001 07:57:33 -0800 (PST) Date: Fri, 9 Mar 2001 07:57:33 -0800 (PST) From: Alessandra Ricca Message-Id: <200103091557.f29FvX726495@pegasus.arc.nasa.gov> Subject: Cluster of PCs for Gaussian To: chemistry@ccl.net Dear CCL members: Thanks to all who replied to my original question: ----------------------------------------------------------- We have two clusters of intel based machines. Cluster 1 * Intel Pentium III 600 MHz CPU with fan * ASUS P3B-F Motheroard * 512MB SDRAM PC100MHz (2x256MB), Cas III Type and Low Profile. * 22GB IBM IDE HDD 7200RPM * 4MB AGP ATI Display Card cluster 2 * (1)Intel Pentium III 800MHz CPU with fan, 256K cache * Intel L440GX+ Dual Pentium III Motherboard * SCSI, Lan and VGA on Board * 1024MB SDRAM PC100MHz (4x256MB), ECC Register * 40GB IBM IDE HDD 7200RPM We ran gaussian98 in parallel using linda on cluster 1 using redhat 6.1 for several months and everything appeared to function perfectly. Cluster 2 came with redhat 6.2, and initially everything seemed to be fine, so cluster 1 was upgraded to 6.2. Under 6.2 gaussian jobs fail on cluster 1 with a relatively short mean time between failure. We have now discovered that cluster 2 also seems to have problems under 6.2, but the mean time between failures is much longer. The failures come in two types: 1) the calculation appears to run but values are all garbage (the values print as "nan") 2) one of the processes dies, most commonly, the message is process 0 failed to complete. Before restoring 6.1 to the machine, does anyone know what this problem is and how to fix it? ------------------------------------------------------------- Here are the answers I got: --------------------------------------------------------------------------- Yes, it looks like the same thing we had on our linux machines. I searched for quite a while suspecting hardware problems, but the kernel shipped with redhat6.2 is bugged and gives random numbers on floating point operations. Upgrade to a newer kernel and try again. Cheers, Peter -- Dr. D.P. Tieleman, Assistant Professor, AHFMR Scholar Department of Biological Sciences, University of Calgary 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4 web: www.ucalgary.ca/~tieleman fax: (403)289-9311 ----------------------------------------------------------------------------- Hi all, We have a five-node, heterogeneous cluster of pentium boxes. All of these have RH 6.0 but the kernel was updated to 2.2.16. Since we don't have pgf77 Gaussian sent us the binaries, so we didn't compile the program. Linda version is 3.1. All is working fine. Many of our calculations take several days to converge and we didn't note any problem related to memory or phantom process. It seems that migrating from RH 6.0 to 6.2 would be the problem (I don't kown why, though). Regards, Reinaldo ----------------------------------------------------------------------------------------- Hi Alessandra I requested some help for the same problem i couple of weeks ago. The problem is the kernel that comes with RH6.2, aparently 6.0 has no problem. You must upgrade to the newest Kernel to correct the problem, I solved the problem upgrading to the whole RH7.0 and gaussian runs nice, and without any problem. I had a lot of problem to upgrade the kernel alone because of an incompatibility with SCSI disk. Now, since you have a couple of clusters you may want to try NWChem, its nice and it's supposed to work really well on multiprocessor tasks. http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html I don't have a lot of experience because i don't have any cluster, but it may be good and it's free and easy to use. You may want to take a look at the web page, it has good info. Best Regards Max --------------------------------------------------------------------------- Everyone running rh6.2 with the stock kernel (2.2.14 something) should upgrade the kernel to either 2.2.16-3 or 2.2.17 something. rh 2.2.14 will give random floating point errors. this is a faq Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ---------------------------------------------------------------------- First I'd just test the hardware really well with memtest86 from sgi. If the memory comes back without errors then we can take the next step and see what compilers you used. If you recompiled g98 after the upgrade. What kernel version you are using under 6.2 vs 6.1 etc... I have g98 running on our 212 proc cluster and have had to work through a lot of the bugs in g98 and linda but have been able to come up with a fairly good working set of binaries. ----------------------------------------------------------------- I advice not to use kernel 2.2.16, it has too many bags. Try to upgrade to 2.2.17 now available. -- Dr. Irena Efremenko Wolfson Department of Chemical Engineering Technion - Israel Institute of Technology Haifa 32000, Israel Phone: 972-4-8293561 Fax: 972-4-8230476 ----------------------------------------------------------------------- Thanks again. Alessandra Alessandra Ricca Mail: NASA Ames Research Center Senior Research Scientist Mail Stop 230-3 ELORET Corporation Moffett Field, CA 94035-1000 http://www.eloret.com Ph: +1-650-604-5410 Email: ricca@pegasus.arc.nasa.gov Fax: +1-650-604-0350 From chemistry-request@server.ccl.net Fri Mar 9 13:38:00 2001 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f29Ic0w10481 for ; Fri, 9 Mar 2001 13:38:00 -0500 Received: from mail.chem.tamu.edu ([165.91.179.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Fri, 9 Mar 2001 12:38:22 -0600 Message-ID: <3AA922E2.24752C4D@mail.chem.tamu.edu> Date: Fri, 09 Mar 2001 12:37:23 -0600 From: lakshmi@mail.chem.tamu.edu (Sahasranaman Mahalakshmi) X-Mailer: Mozilla 4.05 [en] (WinNT; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: (no subject) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I would like to know a website where I could download gunzip executable for IBM machine AIX 3.2. Thank you very much for your help. Thanking You, Mahalakshmi From chemistry-request@server.ccl.net Fri Mar 9 13:57:47 2001 Received: from web5410.mail.yahoo.com (web5410.mail.yahoo.com [216.115.106.202]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f29Ivlw10600 for ; Fri, 9 Mar 2001 13:57:47 -0500 Message-ID: <20010309185747.22752.qmail@web5410.mail.yahoo.com> Received: from [128.97.139.222] by web5410.mail.yahoo.com; Fri, 09 Mar 2001 10:57:47 PST Date: Fri, 9 Mar 2001 10:57:47 -0800 (PST) From: eric hu Subject: summary: software to detect binding site To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers A week ago, I posted a message: > I'm working on a big protein which has multiple > binding domains. Is there a > way to choose the best binding site for the ligand? > Maybe it's just a > dream. Hello, all Thank you very much for the input. I'll give a summary later. My question now is after I find the possible pockets or cavities of a protein, how can I dock the substrate to the pockets effectively? I really hope there is an easier way instead of manually docking with autodock or other tools. Maybe I can use the substrate as a probe to detect those possible binding pockets with easy algorithm such as simply comparing the vdw volume and so on. Then I can get rid of bad condidates quickly. So the question actually is how you narrow down the possible general binding modes for a given substrate. thanks Eric I received a lot of replies. Here I list some of them. And thanks for all the kind people. (1)CastP Eldbjéög Sofie Heimstad Hi Eric, Take a look on CAST: http://cast.engr.uic.edu/cast/ - it may be useful. Mitchell Polley Tripos offers SiteID for identifying potential binding pockets. (www.tripos.com) There is also CAST for this purpose. (http://sunrise.cbs.umn.edu/cast/) (2)Autodock "Zengjian Hu" Hi, Eric I suggest that you use Autodock program developed by Dr. Olson > from the Scripps Research Insititute. It certainly can find the proper binding site in the protein. Best regards, Zengjian "Garrett M. Morris" AutoDock is not a manual docking program: as its name suggests, it is an *automated* docking program. If you create a grid box that is big enough to hold the entire protein/DNA molecule and the ligand, then AutoDock will search the entire molecule for good binding sites. You do not need a priori knowledge of the location of the active site. The most efficient search method in AutoDock is the Lamarckian Genetic Algorithm, which does better than traditional GA and much better than Monte Carlo simulated annealing, given the same number of energy evaluations. See the web site for more information: http://www.scripps.edu/pub/olson-web/doc/autodock/ AutoDock 3.0 is free to academic and non-profit research organisations, and the source code is provided. (3)MOE wolfram@chemcomp.de Hi Eric, the latest version of MOE has a couple of very nice features to a) identify suitable binding sites based on curvature information and interaction patterns b) explore interactions in the binding site and suggest preferred atom locations in de-novo or lead optimization projects If you need more information, pls feel free to contact me at wolfram@chemcomp.de (These features are not yet covered by our webjournal at www.chemcomp.com, as they are just being released). Thanks and have a good day, Wolfram. (4)FlexX David Larson Dear Eric, FlexX and/or SiteID may be what you are looking for. Please take a look at these webpages: FlexX http://www.tripos.com/software/flexx.html SiteID http://www.tripos.com/software/siteid.html Sincerely, Dave Larson "Dr. Dave Winkler" One of the best methods seems to be FlexX. A new paper on this came out today on the ACS ASAP site. The following ASAP articles were posted to the ACS Web Edition of Journal of Medicinal Chemistry on March 6, 2001. Title: Detailed Analysis of Scoring Functions for Virtual Screening Authors: Martin Stahl and Matthias Rarey Link:< http://dx.doi.org/10.1021/jm0003992> http://dx.doi.org/10.1021/jm0003992 Cheers, Dave (5)GRAMM Eldbjéög Sofie Heimstad Hi, Has anybody mentioned the available docking program GRAMM. It is free of charge it is very easy to use. Remember to name all atoms that should be treated by the program with the naming ATOM in the PDB file. HETATM entries are not treated. Look at the high resolution (small ligands) and low resolution docking alternatives. Internet address: http://reco3.musc.edu/gramm/ -eldbjéög (6)others Renxiao Wang As far as I know, people usually determine the binding site by three ways: (1) sometimes they can get the crystal structure of the receptor-ligand complex, so that they know where the binding site is; (2) if not, some biological experiments (such as single-point mutation) may provide indirect evidence. So maybe you need to read more papers searching for such information; (3) binding site is usually more flexible than the other part, so maybe you can color all the atoms by their thermal factors and check where is the "hot" spot. Computational methods are no good for this purpose. You may try AutoDock by setting a very large "box" which can actually cover the whole receptor. Occasionally this trick works. Take it easy. You will get through it anyway. Antonio Luiz Noronha Hi Eric You can use a program to map the surface of your protein, like GRID, and then use any de novo program to design the ligand in the site you find as been the most important. Best Regards ********************* Also there are other replies which talked about the general ideas on detecting general binding modes. Since we don't have that many comercial softwares like FlexX which might be good at this time, the autodock, gramm, cast and other free software can do the similar job. Again, thanks for all the output from this community. Sincerely, -Eric __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Fri Mar 9 14:12:03 2001 Received: from oxmail.ox.ac.uk (oxmail2.ox.ac.uk [163.1.2.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f29JC2w10694 for ; Fri, 9 Mar 2001 14:12:02 -0500 Received: from ermine.ox.ac.uk ([163.1.2.13]) by oxmail.ox.ac.uk with esmtp (Exim 3.12 #1) id 14bSJ1-0002a5-00 for chemistry@ccl.net; Fri, 09 Mar 2001 19:12:03 +0000 Received: from ivan (helo=localhost) by ermine.ox.ac.uk with local-esmtp (Exim 3.13 #1) id 14bSJ0-00073J-00 for chemistry@ccl.net; Fri, 09 Mar 2001 19:12:02 +0000 Date: Fri, 9 Mar 2001 19:12:02 +0000 (GMT) From: "Ivan I. Oleinik" To: chemistry@ccl.net Subject: Re: CCL:DFT for astronomers In-Reply-To: <0G9X00L6LZXD0O@Salicet.ucd.ie> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, In response to my posting today I received numerous responses where people referred to classical texts on theory of DFT like "DFT of Atoms and Molecules" by Parr and Yang, "A chemists guide to DFT" by Koch and Holthausen etc. These books are on my shelf but I did not want to recommend them to my friend-astronomer. He is not going to become an expert in the DFT theory, but just wants to get a grasp of general ideas on much more qualitative level. I thought there are some articles, not the books that you can even recommend to undergraduates that are not majoring in chemistry or physics. This was my original idea to ask for help. Thanks anyway, Ivan. ------------------------------------------------------------------------ Ivan I. Oleinik E-mail : ivan.oleinik@materials.ox.ac.uk Department of Materials University of Oxford Parks Road Oxford OX1 3PH Tel : +44 (0)1865 283325 United Kingdom Fax : +44 (0)1865 273764 ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Mar 9 16:01:35 2001 Received: from mallard.duc.auburn.edu (mallard2.duc.auburn.edu [131.204.2.23]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f29L1Zw11902 for ; Fri, 9 Mar 2001 16:01:35 -0500 Received: from localhost (kwonohy@localhost) by mallard.duc.auburn.edu (8.8.8+Sun/8.7.2) with SMTP id PAA10566 for ; Fri, 9 Mar 2001 15:01:36 -0600 (CST) X-Authentication-Warning: mallard.duc.auburn.edu: kwonohy owned process doing -bs Date: Fri, 9 Mar 2001 15:01:36 -0600 (CST) From: Ohyun Kwon X-Sender: kwonohy@mallard To: chemistry@ccl.net Subject: about B1LYP and BLYP Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters; Could anybody point out that whether I can use B1LYP and BLYP at the Gaussian98 Rev.A7 ? According to thw G98 user's guide, B1LYP can be available, However Gaussian web site indicates that B1LYP is deferred to Rev. B, and the B1LYP and B1PW91 hybrid functionals will appear in Rev. B. of G98. I would appreciate it if you would give some comments on these matters. Thank you in advance. yours, Tommy Kwon Department of Chemistry Auburn University Auburn, AL, 36849 From chemistry-request@server.ccl.net Fri Mar 9 23:25:02 2001 Received: from mumbai3.mtnl.net.in ([203.94.227.53]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2A4P0w13050 for ; Fri, 9 Mar 2001 23:25:00 -0500 Received: from bol.net.in by mumbai3.mtnl.net.in (8.9.1/1.1.20.3/27Mar00-0611PM) id JAA0000002482; Sat, 10 Mar 2001 09:53:19 +0530 (IST) Message-ID: <3AAA5B31.A00F8EF5@bol.net.in> Date: Sat, 10 Mar 2001 22:19:54 +0530 From: Prashant Desai X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Cerius2 descriptor-"E_state_keys" Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am looking for detailed information on a descriptor category "E_state_keys" available with cerius2 for use in deriving a QSAR. Prashant Desai Dept. Pharmaceutical Chemistry Bombay College of Phamacy, University of Mumbai Mumbai.