From chemistry-request@server.ccl.net Wed Oct 2 08:14:14 2002 Received: from yangtze.hku.hk (IDENT:root@[147.8.148.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g92CEDc10885 for ; Wed, 2 Oct 2002 08:14:13 -0400 Received: from localhost (alarry@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id g92CNmt15398 for ; Wed, 2 Oct 2002 20:23:48 +0800 Date: Wed, 2 Oct 2002 20:23:48 +0800 (HKT) From: Wong Lai Ho To: CHEMISTRY@ccl.net Subject: Problem about Using Autodock3.0 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I have encountered few problems when I was using Autodock3.0. 1,When I perform calculations involing Autogrid, it always complains with the following message: "WARNING! Atom type error, can't find type for "-1.2" in typelist "CNOSHXM"." It will give result eventually, but are these results reliable? (If no, how can I fix it?) 2,I have docked a ligand to two proteins with similar structure and active site.(They are the same protein but coming from different animals). I visualize their structural result with CERIUS2. Although they are similar, their final docked energy is very different(-11.7 and 74.5 kcal/mol respectively). Does any users have similar experience and how do you deal with that? I am grateful if you can provide some solutions. Thanks a lot. Yours Sincerely, Larry Wong From chemistry-request@server.ccl.net Wed Oct 2 08:27:05 2002 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g92CR4c11369 for ; Wed, 2 Oct 2002 08:27:04 -0400 Received: from mach.vub.ac.be (mach.ulb.ac.be [164.15.128.3]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id OAA02503; Wed, 2 Oct 2002 14:24:54 +0200 (MEST) for Received: from resu1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id OAA05771; Wed, 2 Oct 2002 14:27:03 +0200 (MET DST) for chemistry@ccl.net Date: Wed, 2 Oct 2002 14:27:03 +0200 (MET DST) Message-Id: <200210021227.OAA05771@mach.vub.ac.be> From: Pierre Mignon To: chemistry@ccl.net Subject: Amber-param-phosphate X-Mailer: Webmail ULB v2.1 Hello, I use Amber since a few weeks and I have problems for the parameterization of a phosphate group such as PO3H - . I defined the type of each atoms but when I try to minimize, it stops because the H and one O are to close. Types : P : P O : O2 O : O2 O : OH H : HO Any suggestions and/or help ? Thank's in advance. Pierre. Mignon Pierre PhD student Free University of Brussel (VUB) Dienst Algemene Chemie (ALGC) Pleinlaan, 2 1050 Brussels Belgium Tel + 32 2 629 35 16 Fax + 32 2 629 33 17 e-mail pmignon@vub.ac.be From chemistry-request@server.ccl.net Wed Oct 2 03:38:23 2002 Received: from mailgate.rz.uni-karlsruhe.de (exim@[129.13.64.97]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g927cNc03069 for ; Wed, 2 Oct 2002 03:38:23 -0400 Received: from rz70.rz.uni-karlsruhe.de (rz70.rz.uni-karlsruhe.de [129.13.97.243]) by mailgate.rz.uni-karlsruhe.de with esmtp (Exim 3.36 #1) id 17we56-0000VR-00; Wed, 02 Oct 2002 09:38:04 +0200 Date: Wed, 2 Oct 2002 09:38:04 +0200 (CES) From: Harald Svedung To: sweta nigam cc: chemistry@ccl.net, Subject: Re: CCL:random no.generation(doubt) In-Reply-To: <003701c2687a$e8382e50$a62813ac@ATCSWETANIGAM> Message-ID: MIME-Version: 1.0 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 g927cNc03070 hello, A random number generator with very little remaining structure in the result of consecutive calls may look like this: function ggubs() cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc c c ggubs c c c purpose - basic uniform (0,1) pseudo-random number c generator c arguments dseed - input/output double precision variable c assigned an integer value in the c exclusive range (1.d0, 2147483647.d0). c dseed is replaced by a new value to be c used in a subsequent call. c c real*8 dseed,c1,c2,ggubs,c3 include 'mpif.h' parameter (c1=2147483647.d+00,c2=2.d+00**(-31),ic3=16807) common/random/dseed dseed=dmod(ic3*dseed,c1) ggubs=c2*dseed i=i+1 5 format(d30.20) return end where dmod(x,y) does the following: DMOD DMOD calculates a longreal number modulus a second longreal number. Declaration FUNCTION DMOD(VAR x,y:LONGREAL):LONGREAL; EXTERNAL; Attributes Parameters: Both arguments are longreal numbers. Result: A longreal number. HP FORTRAN 77/XL: Intrinsic function: Z=DMOD(X,Y). Error: If either of the arguments is a NaN (or the first argument is infinity or the second argument is zero), there are two possible actions. If the INVALID trap is enabled, the message "DMOD(X,Y): ANY OF X AND Y=NaN OR X=INFINITY OR Y=0.0" occurs. Otherwise, the INVALID flag is set. In either case, a quiet NaN is returned. This was tested in the context of phase space sampling for molecular dynamics simulations by some folks in Göteborg like 10 years ago (I havn't got the exact reference at arms length, sorry) and it has been used ever since. for what it's worth ;-) /Harald On Mon, 30 Sep 2002, sweta nigam wrote: > hello > can u help me to find out what r random no.generators ,plz site some examples used in commercial software like tripos or accelrys in their molecular dyanamics suite... > > Thanks n Regards > Sweta > TCS > Dr. Harald Svedung cellphone: +49-175 736 2576 Institut für Physikalische Chemie or: +46-709-223 206 Universität Karlsruhe Fritz-Haber-Weg 4 D-761 28 Karlsruhe Tyskland Tel: +49-721 608 2715 Fax:+49-721 608 6524 From chemistry-request@server.ccl.net Wed Oct 2 04:19:42 2002 Received: from mail.unime.it ([192.167.101.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g928Jfc04454 for ; Wed, 2 Oct 2002 04:19:41 -0400 Received: from conversion-daemon.mail.unime.it by mail.unime.it (iPlanet Messaging Server 5.1 (built May 7 2001)) id <0H3C00401GFCYC@mail.unime.it> for chemistry@ccl.net; Wed, 02 Oct 2002 10:19:36 +0200 (MEST) Received: from pharma.unime.it (pharma.unime.it [192.167.106.20]) by mail.unime.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H3C004I8HSN56@mail.unime.it> for chemistry@ccl.net; Wed, 02 Oct 2002 10:19:36 +0200 (MEST) Received: from pharma.unime.it (pharma [127.0.0.1]) by pharma.unime.it (8.11.6/linuxconf) with ESMTP id g928JUm24895 for ; Wed, 02 Oct 2002 10:19:31 +0200 Date: Wed, 02 Oct 2002 09:19:30 +0100 From: Laura De Luca Subject: AutoDock To: chemistry@ccl.net Message-id: <20021002081930.M72655@pharma.unime.it> MIME-version: 1.0 X-Mailer: Open WebMail 1.70 20020712 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-OriginatingIP: 192.167.106.131 (ldeluca) X-MailScanner: Found to be clean Hi, CClers, I would like to know a way to add more than 6 atom types in the DPF file in the Autodock program. In fact my ligand has more than seven atom types and when I try to run Autodock I get this error message: /usr/local/programs/Autodock3.0.5/dist305/bin/sgi4D.IRIX64_6.5_R10000/auto dock3: ERROR: ERROR: 7 atom types declared in "x”, /usr/local/programs/Autodock3.0.5/dist305/bin/sgi4D.IRIX64_6.5_R10000/auto dock3: Aborting... /usr/local/programs/Autodock3.0.5/dist305/bin/sgi4D.IRIX64_6.5_R10000/auto dock3: Unsuccessful Completion. [2] Exit 255 /usr/local/programs/Autodock3.0.5/dist305/bin/sgi4D.IRIX 64_6.5_R10000/autodock3 ... Thanks Laura -- Laura De Luca, PhD student Dipartimento Farmaco-Chimico Universita'degli Studi di Messina Viale Annunziata 98168 MESSINA ITALY Phone: +39 090 6766464 Fax: +39 090 355613 email: ldeluca@pharma.unime.it From chemistry-request@server.ccl.net Tue Oct 1 17:10:44 2002 Received: from titan.gcrc.upenn.edu ([130.91.42.69]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g91LAic09199 for ; Tue, 1 Oct 2002 17:10:44 -0400 Received: (from nobody@localhost) by titan.gcrc.upenn.edu (8.11.6/8.11.6) id g91LQbX84755 for chemistry@ccl.net; Tue, 1 Oct 2002 17:26:37 -0400 (EDT) (envelope-from sutjano@pharm.med.upenn.edu) X-Authentication-Warning: titan.gcrc.upenn.edu: nobody set sender to sutjano@pharm.med.upenn.edu using -f Received: from 130.91.168.63 ( [130.91.168.63]) as user sutjano@pharm.med.upenn.edu by www.gcrc.upenn.edu with HTTP; Tue, 1 Oct 2002 17:26:37 -0400 Message-ID: <1033507597.3d9a130db1e0d@www.gcrc.upenn.edu> Date: Tue, 1 Oct 2002 17:26:37 -0400 From: sutjano@pharm.med.upenn.edu To: chemistry@ccl.net Subject: adumb in charmm MIME-Version: 1.0 Content-Type: text/plain; charset=Big5 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.1 Greetings, I have a few questions about the adaptive umbrella application (adumb) in charmm that I was hoping someone can answer. i) There is a note in the ENERGY subroutine stating that the pmf is determined prior to the evaluation of Ewald K-space sum. There seem to be no mention of this in the documentations. Has anyone else attempted the use of Ewald sum with adumb? ..or is adumb strictly limited to the use of cutoffs? ii) There also seem to be a conflict between adumb and the use of NTRFRQ during dynamics to stop trans/rotation of the system. The use of this flag results in a call to the ENERGY subroutine at every NTRFRQ'th step. Since the statistics is collected at every energy calls (rather than at every dynamic steps), there is an over accounting of the umbrella coordinate at every NTRFRQ'th step. Has this issue perhaps been resolved in later version? (I am using version c27b2.) I truly appreciate any input on these matters. Thanks. Jano From chemistry-request@server.ccl.net Wed Oct 2 08:54:23 2002 Received: from jivdhan.unipune.ernet.in ([196.1.114.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g92CsHc12069 for ; Wed, 2 Oct 2002 08:54:21 -0400 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.11.6/8.11.6) with ESMTP id g92Cs1a29142 for ; Wed, 2 Oct 2002 18:24:01 +0530 Received: from localhost (sysadmin@localhost) by chem.unipune.ernet.in (8.9.3/8.8.7) with ESMTP id SAA13913 for ; Wed, 2 Oct 2002 18:19:20 +0530 Date: Wed, 2 Oct 2002 18:19:20 +0530 (IST) From: To: chemistry@ccl.net Subject: lit. on QM methods for studying molecular crystals Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: Can someone point me to a source on the complete literature of methods available for ab initio/semi-empirical calculations on molecular crystals. Thanks in advance Babu _______________________ Ph.D. Student \ Department of Chemsitry \ University of Pune \ PUNE -411 007 / INDIA / _______________________/ From chemistry-request@server.ccl.net Wed Oct 2 03:10:29 2002 Received: from amiram2.md.huji.ac.il ([132.64.165.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g927ASc02510 for ; Wed, 2 Oct 2002 03:10:28 -0400 Received: from amiram2.md.huji.ac.il (localhost.localdomain [127.0.0.1]) by amiram2.md.huji.ac.il (8.11.6/8.11.6) with ESMTP id g927BI604128; Wed, 2 Oct 2002 10:11:18 +0300 Content-Type: text/plain; charset="iso-8859-1" From: Boris Gorelik To: "sweta nigam" , Subject: Re: CCL:random no.generation(doubt) Date: Wed, 2 Oct 2002 10:11:18 +0300 User-Agent: KMail/1.4.3 Cc: References: <003701c2687a$e8382e50$a62813ac@ATCSWETANIGAM> In-Reply-To: <003701c2687a$e8382e50$a62813ac@ATCSWETANIGAM> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200210021011.18560.bgbg@md.huji.ac.il> I highly recomend ou to read "random numbers" chapter (chapter no 7) in "numerical recipies in C" http://www.ulib.org/webRoot/Books/Numerical_Recipes/bookcpdf.html You can try the "GNU scientific library (http://www.gnu.org/software/gsl/gsl.html) which also has couple of random numbers generators and it is well documented (and is a free software) On Monday 30 September 2002 15:14, sweta nigam wrote: > hello > can u help me to find out what r random no.generators ,plz site some > examples used in commercial software like tripos or accelrys in their > molecular dyanamics suite... > > Thanks n Regards > Sweta > TCS -- Boris Gorelik Wed, 02/Oct/2002, 26 Tishrey 5763 ------------------------------------------------- ! Molecular Modelling Group ! ! Pharmacy School, Hadassa Faculty of medicine ! ! The Hebrew University of Jerusalem ! ! http://www.md.huji.ac.il/models/group.html ! ! !------------------------------------------------ From chemistry-request@server.ccl.net Wed Oct 2 12:16:42 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g92GGgc18587 for ; Wed, 2 Oct 2002 12:16:42 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id g92GGhb17971; Wed, 2 Oct 2002 12:16:43 -0400 (EDT) Date: Wed, 2 Oct 2002 12:16:42 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: Spam on CCL and my appeal for your help Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Subscribers... Some of you may have noticed that I was out of the country for over 3 weeks. But of course, my "caring eye" {:-)} was with CCL most of the time whenever I could plug myself into some "wire". Few appeals, warnings, etc... We fight spam diligently, but it is not an easy fight. CCL is on any possible spammers list in the world, and we get at times a 1000 spam messages a day. Price of fame and glory {:-)}. Of course you do not see it much... But it is a constant struggle... Spammers devise more sophisticated exploits, and we counter them... It takes resources... Please read on, and at the end, I will tell you what to do, in case when your legitimate message is being bounced back from CCL. But now, an APPEAL FOR HELP... Our funding from federal and state sources reflects a well known trend. Our costs and resources usage are up, while our support is down. The long term outlook does not look good, either, and it would be a pity, if CCL had to go after so many years of fruitful operation. But I am very positive that you will help, and we can prove to our parent organization that we are an important asset. OSC is very generous and provides us with high-bandwidth Internet connection, IP address space, office space, technical support, etc., etc., at no cost, but expect as to cover at least some of personnel and hardware costs. PLEASE HELP NOW!!! You can help in a number of ways: 1) Give us a DONATION (tax deductible in US and many other countries). Small donations are welcome! We will gladly take many $20 donations. Make check to "OSC Development Fund (CCL)" and send check to me: Jan Labanowski, OSC, 1224 Kinnear Rd, Columbus, OH 43212-1163, USA We will add you to the CCL Sponsors Page at: http://www.ccl.net/cgi-bin/donors You can also do a bank transfer, or FAX us a simple Credit Card form to: 614-688-3998 (secure FAX in OSC Business office). Donation for CCL in the amount of:.................... US Dollars Card: Visa/MC Your Name: Your Address: [We need it to send you the a Thank you letter for Tax Purposes, since your donation may be TAX Deductible] Card Number: Expiration Month/Year: Signature: You will get a letter confirming your donation for tax purposes. For bigger (1000 USD or more) donations we will put your logo and link on the CCL page of your choice as our way of saying Thank You!!! If you need a supporting letter from CCL, or more details, do not hesitate to contact Jan Labanowski at jkl@ccl.net. 2) PURCHASE THE CCL ARCHIVES from us. You will have a set of 4 CDs which contain all files, software, and messages from CCL archive. They can be easily searched with grep or whatever. They are $250 for a set. You can also purchase multiple sets. We offer a regular billing procedure, so you can pay from your grant or other institutional funds by PO, check, credit card, wire, etc. Details can be found at: http://www.ccl.net/chemistry/aboutccl/supporting/services 3) ADVERTISE YOUR JOB OPPORTUNITIES with us, and if you are successful, please send us $100. We are being praised for capturing attention of selective audience which uses computers in chemistry, life sciences, and materials design. We are told that we bring more CVs than ads in traditional trade publications at a fraction of the cost. Paying for our service is voluntary and on honor basis. Pay if you can. More details: http://www.ccl.net/jobs Now... More about the spam defenses... We use several layers. Basically, we collect spam messages and then extract IP addresses of spammers from the headers with scripts. Then, we block the subnets with 3 first octets of the spammer. Our latest spammers list is available at: http://www.ccl.net/spammers.txt (we cannot advertize it for legal purposes, but you are a member). Check, if your mail gateway is there by any chance Yes, we know, it is radical, and innocent blood is being spilled. If some hackers invaded one of your departmental computers, and spammed us, your innocent computer will be blocked. If your message bounces as: "Access denied" it means that your computer was blacklisted as a spam generator. Send the copy of your mail to jkl@ccl.net, and I will usually remove your computer from the black list, and resend your message to CCL. Please do not hesitate to do this... We really want your messages appear on CCL, and we are here to help. At the same time, imagine what would happen if the spam was appearing on CCL. This is a painful compromise... Sorry... The blacklisting of IP addresses is the reactive measure (we had to be spammed first to add it to a blacklist). We also use the pro-active measures. Our distribution script checks a large dictionary of words commonly found in spam messages. We also check the consistency of e-mail header lines. Note, we do not check if message comes from a subscriber of CCL. We get many subscriptions from people which we suspect are prospective spammers. We do not have resources to do "background checks" and have a policy to sign up everyone, THOUGH WE PREFER THAT YOU SEND US YOUR SUBSCRIPTION FROM AN INSTITUTIONAL ADDRESS. Sometimes legitimate messages are being stopped since they contain words which may imply spam (e.g., sex vs. spin sextet state). The messages rejected this way are reviewed, usually at least once a day, and resent if found legitimate. Unfortunately, the students working for CCL are not computational chemists, and are asked to act with "extreme prejudice". If your message does not appear on CCL within two days, please bug me directly: jkl@ccl.net (send me an original message) and I will resent it. There are also many other tests which are done on the messages (e.g., for possible viruses, and hidden junk in attachments). It is constant fight to get ahead of the latest devices of evil forces of the Internet. We hope that this is working for the common good, and that our effort is worth it. We would hate to send a single message with a malicious virus and infect a few thousands computers with a single mistake. You can help us a lot by sending plain text, unencoded mail, with no attachments. In most cases this is what you really want. Please understand that when your message is stopped or bounced, it is nothing personal. We try to do our best and defend the CCL against malice, naivete (e.g., those poor kids hoping to earn millions on spamming people with junk mail which nobody reads), oversight, and irresponsibility of some Internet users. When we review messages, the address of the from line is our list consideration, as it is easily forged. Some final advice... If you get a spam message, and it says: send request to UNSUBSCRIBE from our service, do not send any requests. They just want a confirmation that your address is valid, and that you received their junk mail. Also, do not open any attachments when you are not ABSOLUTELY SURE that they are safe. Do not always trust the originator e-mail address. People ask me often while that get the e-mail from jkl@ccl.net which advertises "teen site". It did not come from me... Someone forged mail headers and used my address hoping that you will recognize it and open the message. To really see where your message is coming from, you need to look at the top Received: line of the header of your message. While it is easy to do under UNIX with most mail readers, the MS products will usually not allow you to easily look at headers (they want to keep it EASY -- but the problem is that it AIN'T EASY). Thank you for your attention and help... Jan Labanowski, jkl@ccl.net The CCL Keeper... Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | E-mail: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/~jkl Columbus, OH 43212-1163 | http://www.ccl.net/ http://asdn.net/ From chemistry-request@server.ccl.net Wed Oct 2 17:50:07 2002 Received: from mole.chem.iupui.edu ([134.68.136.192]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g92Lo7c28584 for ; Wed, 2 Oct 2002 17:50:07 -0400 Received: from chem.iupui.edu ([134.68.137.128]) by mole.chem.iupui.edu (8.9.1/8.9.1) with ESMTP id QAA1610666; Wed, 2 Oct 2002 16:49:41 -0500 (EST) Message-ID: <3D9B69C4.EF1EC3D0@chem.iupui.edu> Date: Wed, 02 Oct 2002 16:48:54 -0500 From: "Boyd, D." X-Mailer: Mozilla 4.79C-CCK-MCD {C-UDP; EBM-APPLE} (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: OSC CCL Subject: GRC on Computational Chemistry Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear CCLers, The website for the Gordon Research Conference on Computational Chemistry has been revamped and updated. Included is news about the 2002 conference and the group photo of the participants. Of particular interest is the fact that Dr. Bill Swope (IBM) will be Chair of the 2004 conference. And Prof. Wilfred van Gunsteren was elected to be Vice-chair in 2004 and hence Chair in 2006. The URL is http://chem.iupui.edu/rcc/grccc.html Thanks, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Department of Chemistry Indiana University-Purdue University at Indianapolis Indianapolis, Indiana 46202-3274, U.S.A. E-mail boyd@chem.iupui.edu