From chemistry-request@server.ccl.net Fri May 25 09:35:46 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4PDZjS05685 for ; Fri, 25 May 2001 09:35:46 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id JAA06936; Fri, 25 May 2001 09:35:45 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 25 May 2001 09:35:58 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GDW00IFG8898M@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Fri, 25 May 2001 09:31:21 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Fri, 25 May 2001 09:35:54 -0400 Content-return: allowed Date: Fri, 25 May 2001 09:35:45 -0400 From: "Shobe, Dave" Subject: RE: CCL:CAS Registry Numbers algorithm To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAAF16@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 I made a slight but important mistake: "prime relative to the base" should be "relatively prime to the base". I.e. the numbers that do not share commmon factors with the base (except for 1 of course). The advantage of using a prime number base (such as 11 in ISBN) is that there are fewer non-relatively-prime-to-the-base numbers. However, base 10 has the advantage of not introducing extra symbols into the character set (like the X in ISBN). Actually it's pretty easy to design an algorithm that "catches" more errors: simply use two digits. The first digit could be from the current algorithm, which will catch any transposition; the second digit could simply be the sum of all the digits, modulo 10, which would catch any single substitution. You might even be able to design one that catches a single digit omission as well. However, the saying that nothing is foolproof given the constant ingenuity of fools comes to mind. --Dave "Shobe, Dave" wrote: > Come to think of it: the algorithm might catch transposition errors, but a > single-digit error such as 5555-31-7 vs. 5555-81-7 would not be detected, if > the digits differ by 5 in an even position, or if they differ by an even > number in the 5th position. > > The ISBN algorithm doesn't have this problem since 11 is prime. However any > error the 11th digit would be completely undetectable. You could fix this I > suppose by only using digit multipliers that are prime relative to the base. > > Thus an improved(?) CAS RN algorithm would take 1234-31-? and calculate > 1*1+3*3+4*7+3*9+2*11+1*13. However, now the multiplers for adjacent digits > would differ by 2 or 4 instead of 1, and a transposition of the type > 5555-38-7 vs. 5555-83-7 would not be detected since 3*8+3=27 and 3*3+8=17. From chemistry-request@server.ccl.net Fri May 25 09:23:10 2001 Received: from mail.fqspl.com.pl ([212.244.147.7]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f4PDN5S05372 for ; Fri, 25 May 2001 09:23:06 -0400 Received: (qmail 17610 invoked from network); 25 May 2001 15:24:13 -0000 Received: from test.fqspl.com.pl (HELO test) (10.10.10.50) by fqspl.com.pl with SMTP; 25 May 2001 15:24:13 -0000 Message-ID: <008a01c0e51e$1f5975b0$320a0a0a@fqspl.com.pl> From: "Victor Anisimov" To: Subject: Circular Dichroism survay Date: Fri, 25 May 2001 15:25:10 +0200 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear Chemists, Some time ago I posted a message asking people to fill a Circular Dichroism questionnaire form. I'm very grateful to everyone who replied. All your responses are carefully reviewed and taken into account. The results of the review do not seem to be of everyone's interest therefore I publish only a list of respondents who won the free software as we promised it in our announcement. The winners are: MOPAC2000 for Windows: Prof. Robert Latour, Dept. of Bioengineering, Clemson University, U.S.A. Quantum CAChe for Windows: Mr. Branko Kolaric, PhD student, Institute fur Chemie, Stranski laboratorium, TU-Berlin, Germany All other respondents are granted by discounts on Fujitsu Computational Chemistry software. With kind regards, Victor Anisimov. ================================================== Victor Anisimov, PhD, Senior Software Researcher - Computational Chemist FQS Poland, a Fujitsu company ul. Starowislna 13-15, 31-038 Krakow, Poland Email: victor@fqspl.com.pl Tel.(+48 12) 429-4345 Fax(+48 12) 429-6124 ================================================== From chemistry-request@server.ccl.net Fri May 25 05:31:28 2001 Received: from hotmail.com ([209.185.241.35]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4P9VOS04114 for ; Fri, 25 May 2001 05:31:27 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 25 May 2001 02:31:16 -0700 Received: from 130.120.89.37 by lw3fd.law3.hotmail.msn.com with HTTP; Fri, 25 May 2001 09:31:16 GMT X-Originating-IP: [130.120.89.37] From: "Gustavo Velardez" To: chemistry@ccl.net Subject: Compilation problems II Date: Fri, 25 May 2001 09:31:16 -0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 25 May 2001 09:31:16.0661 (UTC) FILETIME=[72952650:01C0E4FD] Hi everybody, thank you to the people that answered my first question about the compilation problems on Gaussian 98 A7 in a PC with Red Hat Linux 7.1. I fix the first error on the compilation but there is another one: .... ranlib l302.a gau-cpp -I/home/gust/g98 -I/home/gust/g98s -DGAUSS_PAR -DGAUSS_THPAR -DDEFMAXSHL=20000 -DDEFMAXATM=20000 -DDEFMAXNZ=20000 -DDEFNVDIM=257 -DDEFARCREC=1024 -DMERGE_LOOPS -DUSE_ESSL -D_I386_ -DLITTLE_END -DUSING_F2C -DDEFMAXIOP=100 -DDEFMAXCHR=1024 -DDEFLMAX=13 -DDEFN3MIN=10 -DDEFMAXHEV=2000 -DDEFCACHE=64 -DDEFMAXLECP=10 -DDEFMAXFUNIT=5 -DDEFMAXFFILE=10000 -DDEFMAXFPS=1300 -DDEFMAXINFO=200 -DDEFMAXOP=120 -DDEFMAXTIT=100 -DDEFMAXRTE=4000 -DDEFMAXOV=500 -D_ALIGN_CORE_ -DCA1_DGEMM -DCA2_DGEMM -DCAB_DGEMM -DLV_DSP -DO_BKSPEF -DDEFMXTS=1500 -DDEFMXBAS=500 -DDEFMXOPT=50 -DDEFMXBOND=12 -DDEFMXSPH=250 -DDEFMXINV=1500 ml302.F ml302.f pgf77 -O2 -tp p6 -Munroll -Mvect=cachesize:524288 -c ml302.f rm -f ml302.f ml302.c make[1]: Leaving directory `/home/gust/g98' pgf77 -O2 -tp p6 -Munroll -Mvect=cachesize:524288 -o l302.exe ml302.o utilPSNL.o PSNL.o EGP.o l302.a bdrys.o util.so /usr/bin/ld: cannot open utilPSNL.o: No such file or directory make: *** [l302.exe] Error 1 endif .... -------------------------------------------------------------------- and the compilation is stopped. Thank you for your attention. Gustavo Velardez PhD LCAR-IRSAMC. Université Paul Sabatier. 118 route de Narbonne. 31062. Toulouse. France. TE: +33-(0)5-61-55-60-09 FAX:+33-(0)5-61-55-83-17 _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From chemistry-request@server.ccl.net Fri May 25 10:35:43 2001 Received: from mail.shcnc.ac.cn ([202.127.16.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4PEZfS07538 for ; Fri, 25 May 2001 10:35:42 -0400 Received: from PC18 ([202.127.19.225]) by mail.shcnc.ac.cn (8.9.3/8.9.3) with SMTP id WAA19980 for ; Fri, 25 May 2001 22:34:39 +0800 (CDT) Message-Id: <200105251434.WAA19980@mail.shcnc.ac.cn> Date: Fri, 25 May 2001 22:30:40 +0800 From: bxiong To: "chemistry@ccl.net" Subject: X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit hello,all members: I am a new AMBER user, when I use this program ,I find my protein pdb file has the organic ligand , I did not the parameters of the ligand . Can someone help me to tell where have the parameters database or files ?thanks a lot! I will summarize the answers. Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office) From chemistry-request@server.ccl.net Fri May 25 09:42:37 2001 Received: from tech.chem.ethz.ch ([129.132.124.253]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4PDgaS05898 for ; Fri, 25 May 2001 09:42:36 -0400 Received: from tech.chem.ethz.ch (baiker8.ethz.ch [129.132.125.8]) by tech.chem.ethz.ch (8.8.8/8.8.8) with ESMTP id PAA06252 for ; Fri, 25 May 2001 15:42:34 +0200 (CEST) Message-ID: <3B0E65B6.518CEABD@tech.chem.ethz.ch> Date: Fri, 25 May 2001 16:01:26 +0200 From: angelo vargas Organization: ETHZ X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: Computational Chemistry List Subject: Gaussian error message on charges fitted to el. potential Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all a colleague was trying to calculate charges fitted to electrostatic potential on a complex containing a Platinum atom, using the Gaussian program with the following input: #BP86/LanL2DZ gfinput Pop=CHelp Guess=(Read,Only) Density=Checkpoint GEOM=Checkpoint and got the following error message Francl (CHELP) atomic radii used. GetVDW: no radius for atom 1 atomic number 78. Error termination via Lnk1e in /usr/c4/sw/chempool/g98/l602.exe. evidently the program was looking for a vdw radius for Pt and could not find it . The same problem occurs using Pop= MK Is there a way to introduce the VdW radius for Pt or another way of making the program calculate the charges (fiited to elp) (I mean with Gaussian, I know you can do it using other programs) ? Thanks and have a nice day Angelo -- _______________________________________________________________________ Angelo Vargas Laboratory of Technical Chemistry Department of Chemical Engineering and Industrial Chemistry Swiss Federal Institute of Technology (ETHZ) ETH Zentrum, Universitätsstr. 6 Telefon: 0041/1/632 31 54, Room CNB B98.3 CH-8092 Zürich - Switzerland Fax: 0041/1/632 11 63 E-mail: vargas@tech.chem.ethz.ch http://mercury.ethz.ch/HOMEPAGE/members/vargas/vargas.html ________________________________________________________________________ From chemistry-request@server.ccl.net Fri May 25 12:24:18 2001 Received: from socrates.cgl.ucsf.edu ([128.218.27.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4PGOIS10850 for ; Fri, 25 May 2001 12:24:18 -0400 Received: (from ross@localhost) by socrates.cgl.ucsf.edu (8.9.3/8.9.3/GSC1.7) id JAA16843; Fri, 25 May 2001 09:24:14 -0700 (PDT) Date: Fri, 25 May 2001 09:24:14 -0700 (PDT) From: Bill Ross Message-Id: <200105251624.JAA16843@socrates.cgl.ucsf.edu> To: bxiong@mail.shcnc.ac.cn Subject: Re: CCL:X-mailer: FoxMail 3.0 beta 2 [cn] Cc: chemistry@ccl.net I am a new AMBER user, when I use this program ,I find my protein pdb file has the organic ligand , I did not the parameters of the ligand . Can someone help me to tell where have the parameters database or files ?thanks a lot! I will summarize the answers. See "Developing new parameters" on the amber web or mirror: http://amber.ucsf.edu/amber/newparams.html http://amber.ch.ic.ac.uk/newparams.html Bill Ross From chemistry-request@server.ccl.net Fri May 25 14:09:56 2001 Received: from web13205.mail.yahoo.com ([216.136.174.190]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f4PI9uS13209 for ; Fri, 25 May 2001 14:09:56 -0400 Message-ID: <20010525180954.81149.qmail@web13205.mail.yahoo.com> Received: from [129.105.55.29] by web13205.mail.yahoo.com; Fri, 25 May 2001 11:09:54 PDT Date: Fri, 25 May 2001 11:09:54 -0700 (PDT) From: mike smith Subject: Temperature fluctuation during a const T simulation To: chemistry@ccl.net In-Reply-To: <3B0E748B.B93C5A85@iris.sipp.ac.cn> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear listers, In molecular dynamics, there are a lot of techniques to keep the Temperature(T) constant, such as velocity scaling, NOSE heat bath, Langevin dynamics, and so on. However, as you know that the T can't always be a constant, but fluctuating around the input value. I am doing a simulation by Langevin dynamics, and my trouble is that the T fluctuation of my results is very big (The variance of T is about 50K). I think this will weaken any of my conclusions based on the simulation, especially for those temperature senstive quantuties. Since I don't have much experience on Langevin dynamics, I am wondering if anyone could give me some help on how to MINIMIZE the temperature fluctuation for Langevin dynamics. Thanks a lot in advance. Sincerely, Mike Smith __________________________________________________ Do You Yahoo!? Yahoo! Auctions - buy the things you want at great prices http://auctions.yahoo.com/ From chemistry-request@server.ccl.net Fri May 25 14:21:28 2001 Received: from oulu.fi (root@[130.231.240.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4PILSS13397 for ; Fri, 25 May 2001 14:21:28 -0400 Received: from cc.oulu.fi (lensink@sun3.oulu.fi [130.231.240.13]) by oulu.fi (8.8.5/8.8.5) with ESMTP id VAA28497; Fri, 25 May 2001 21:21:26 +0300 (EET DST) Received: (from lensink@localhost) by cc.oulu.fi (8.8.5/8.8.5) id VAA06112; Fri, 25 May 2001 21:21:26 +0300 (EET DST) Message-Id: <200105251821.VAA06112@cc.oulu.fi> Subject: Re: CCL:Gaussian error message on charges fitted to el. potential In-Reply-To: <3B0E65B6.518CEABD@tech.chem.ethz.ch> from angelo vargas at "May 25, 2001 04:01:26 pm" To: angelo vargas Date: Fri, 25 May 2001 21:21:26 +0300 (EET DST) CC: Computational Chemistry List From: Marc Lensink Reply-To: marc.lensink@oulu.fi X-Mailer: ELM [version 2.4ME+ PL66 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit angelo vargas wrote: > > #BP86/LanL2DZ gfinput Pop=CHelp Guess=(Read,Only) > Density=Checkpoint GEOM=Checkpoint > > Francl (CHELP) atomic radii used. > GetVDW: no radius for atom 1 atomic number 78. > Error termination via Lnk1e in /usr/c4/sw/chempool/g98/l602.exe. > > Is there a way to introduce the VdW radius for Pt or another way of making the program calculate the charges Have a look at manual on the gaussian webpage, I believe you have to add ReadRadii to the keyword section and after the molecule definition put an empty line followed by 'Pt 3.5' (or whatever radius you want to give it. Check that webpage, it has loads of info. Furthermore, I'm not exactly sure if my syntax is correct. http://208.192.129.32/g98.htm Marc -- Marc Lensink http://www.biochem.oulu.fi/~lensink/ dept of Biochemistry, Biocenter, University of Oulu PO Box 3000, 90014 Oulu, Finland tel +358 8 553 1139 fax +358 8 553 1141 From chemistry-request@server.ccl.net Fri May 25 15:24:20 2001 Received: from heimdal.compchem.ucsf.edu ([128.218.68.75]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4PJOKS14723 for ; Fri, 25 May 2001 15:24:20 -0400 Received: from localhost (caldwell@localhost) by heimdal.compchem.ucsf.edu (8.11.0/8.10.2) with SMTP id f4PIAtM01810; Fri, 25 May 2001 11:10:55 -0700 (PDT) Date: Fri, 25 May 2001 11:10:55 -0700 (PDT) From: jim caldwell To: amber@heimdal.compchem.ucsf.edu cc: chemistry@ccl.net Subject: Peter Kollman Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Professor Peter A. Kollman of the Universty of California at San Francisco died early on the morning of May 25 following a short illness from cancer. Our condolences to his family. An announcement will be made concerning memorial services. Contact: Peggy Kaplan, School of Pharmacy Dean's Office, 415 476 8010 ---------------------------------------------------------------------------- James W. Caldwell (voice) 415-476-8603 Department of Pharmaceutical Chemistry (fax) 415-502-1411 Mail Stop 0446 (email) caldwell@heimdal.ucsf.edu 513 Parnassus Avenue University of California San Francisco, CA 94143-0446 ---------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri May 25 16:03:46 2001 Received: from freyr.chem.washington.edu (IDENT:root@[128.95.128.138]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4PK3kS15911 for ; Fri, 25 May 2001 16:03:46 -0400 Received: from localhost (fer@localhost) by freyr.chem.washington.edu (8.11.0/8.11.0) with ESMTP id f4PK1NM09959 for ; Fri, 25 May 2001 13:01:23 -0700 Date: Fri, 25 May 2001 13:01:23 -0700 (PDT) From: "Fernando D. Vila" To: Computational Chemistry List Subject: Electrostatic Interaction Energy Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers; I need to calculate the electrostatic interaction energy between to monomers in a dimer but using the wavefunction of each isolated monomer. I have written a small code that uses an electron density grid to do this (a cube file from Gaussian) but have run into some problems. First, the number of points in the grid has to be quite large to avoid having integration problems. Second, for those large grids, the program is extremely slow because of all the pairs of points it has to consider. I have started to write another code that would calculate the energy analytically, but this is not a very simple thing to do. I was wondering if anybody knew of a program that could do this, or if there is any way of tricking common programs like Gaussian into calculating the ES interaction energy. Thanks in advance, Fer. ******************************************************************************* Fernando D. Vila Voice (206)616-3207 Department of Chemistry Fax (206) University of Washington E-mail fer@freyr.chem.washington.edu Seattle, WA 98195, USA WWW ******************************************************************************* From chemistry-request@server.ccl.net Fri May 25 16:11:38 2001 Received: from mail.chem.tamu.edu ([165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4PKBcS16178 for ; Fri, 25 May 2001 16:11:38 -0400 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, 25 May 2001 15:12:47 -0500 Message-ID: <3B0EBC51.7B99016B@mail.chem.tamu.edu> Date: Fri, 25 May 2001 15:10:57 -0500 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 CCLer's, does anybody have a program which solves the ordinary eigenvalue equation for a real nonsymmetric matrix but giving only a few eigenvalues (above zero, i.e. from zero to 20 ) and the size of the matrix is 3000*3000 ? If you do know any site from which I can procure a program like this, please let me know. Thanking You, Mahalakshmi From chemistry-request@server.ccl.net Fri May 25 17:29:53 2001 Received: from umbi3.umbi.umd.edu ([136.160.7.51]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4PLTrS17772 for ; Fri, 25 May 2001 17:29:53 -0400 Received: from umbi.umd.edu (hatter.carb.nist.gov [129.6.113.76]) by umbi3.umbi.umd.edu (Netscape Messaging Server 4.15) with ESMTP id GDWUEX00.D9Y for ; Fri, 25 May 2001 17:30:33 -0400 Message-ID: <3B0ECEEE.B36AAAFA@umbi.umd.edu> Date: Fri, 25 May 2001 17:30:22 -0400 From: "Michael K. Gilson" X-Mailer: Mozilla 4.77 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Binding Databases Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, In April, I asked for leads on academic or commercial databases with measured binding affinities other than ProNIT, DIP, BIND, the Ligand-Protein Database, and BindingDB. No one reported in with any other databases like this. Also, I checked with MDL and CAS, and neither of them have a database like this. Regards, Mike