From chemistry-request@server.ccl.net Fri Oct 18 03:55:52 2002 Received: from mail.szote.u-szeged.hu ([160.114.96.63]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9I7tpi23075 for ; Fri, 18 Oct 2002 03:55:51 -0400 Received: from ovrisc.mdche.u-szeged.hu (IDENT:qmailr@ovrisc.mdche.u-szeged.hu [160.114.101.224]) by mail.szote.u-szeged.hu (8.9.3/8.8.7) with SMTP id JAA01692 for ; Fri, 18 Oct 2002 09:55:50 +0200 Received: (qmail 23935 invoked by uid 525); 18 Oct 2002 07:55:50 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 18 Oct 2002 07:55:50 -0000 Date: Fri, 18 Oct 2002 09:55:50 +0200 (CEST) From: To: Carsten Detering cc: chemistry@ccl.net Subject: Re: CCL:charges on receptor and docking In-Reply-To: <006801c2756a$fc9372e0$74805f80@donald> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Carsten, Gasteiger charges are generally smaller in their values than e.g. Amber charges. Consequently, you get smaller energies for the electrostatic non-bonding term and for the calculated dG, as well. In my oppinion docking energy values should not be directly compared to dG values obtained from experiments (via Ki determination), even if sometimes there are very good agreement in the quantity of them. Docking dGs are rather good for relative comparisons in a set of complexes/ligands, ligand database screening, etc. Best wishes, Csaba From chemistry-request@server.ccl.net Fri Oct 18 09:25:47 2002 Received: from smtp7.andrew.cmu.edu ([128.2.10.87]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9IDPli31156 for ; Fri, 18 Oct 2002 09:25:47 -0400 Received: from UNIX13.andrew.cmu.edu (UNIX13.andrew.cmu.edu [128.2.11.213]) (user=cramirez mech=KERBEROS_V4 (0 bits)) by smtp7.andrew.cmu.edu (8.12.3.Beta2/8.12.3.Beta2) with ESMTP id g9IDPlBI009213 for ; Fri, 18 Oct 2002 09:25:47 -0400 Date: Fri, 18 Oct 2002 09:25:47 -0400 (EDT) From: Carlos Andres Ramirez-Mondragon To: chemistry@server.ccl.net Subject: Modifying a dihedral in CHARMM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello. I'm new to the list and I'm hoping someone could help me with modifying a dihedral angle in CHARMM. I would like to modify my alpha helical peptide to a beta-sheet. Any suggestions are welcome, as it would be more than what I know now. Thank you. Carlos A. Ramirez-Mondragon cramirez@andrew.cmu.edu From chemistry-request@server.ccl.net Thu Oct 17 16:13:08 2002 Received: from hotmail.com ([64.4.37.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HKD7f00818 for ; Thu, 17 Oct 2002 16:13:08 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 17 Oct 2002 13:13:07 -0700 Received: from 138.23.156.82 by pv2fd.pav2.hotmail.msn.com with HTTP; Thu, 17 Oct 2002 20:13:07 GMT X-Originating-IP: [138.23.156.82] From: "Donald Keidel" To: chemistry@ccl.net Subject: Kd vs. potential energy Date: Thu, 17 Oct 2002 13:13:07 -0700 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 17 Oct 2002 20:13:07.0998 (UTC) FILETIME=[9BCD53E0:01C27619] Hello all, I am currently docking ligands to a protein and determining the final potential energy of the system. I thought (although foolishly) that I could correlate the Kd determined experimentally with the finbal potential energy. However, this is not the case. Does anyone know how people correlate Kd with energies. I know this is a real general question, but any suggestions are appreciated. Thank you and have a great day. Don Keidel _________________________________________________________________ Surf the Web without missing calls! Get MSN Broadband. http://resourcecenter.msn.com/access/plans/freeactivation.asp From chemistry-request@server.ccl.net Thu Oct 17 13:54:38 2002 Received: from mail3.uno.edu ([137.30.97.220]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HHsaf30813 for ; Thu, 17 Oct 2002 13:54:37 -0400 Received: from uno.edu ([137.30.117.189]) by mail3.uno.edu with Microsoft SMTPSVC(5.0.2195.4905); Thu, 17 Oct 2002 12:54:33 -0500 Message-ID: <3DAEF869.EB51AC9@uno.edu> Date: Thu, 17 Oct 2002 12:50:41 -0500 From: "=?iso-8859-1?Q?M=F3nica?= C. Concha" X-Mailer: Mozilla 4.73 (Macintosh; U; PPC) X-Accept-Language: en,pdf,es MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: parallel quantum solutions Content-Type: multipart/mixed; boundary="------------29E7F667DF923B42649B7D70" X-OriginalArrivalTime: 17 Oct 2002 17:54:33.0680 (UTC) FILETIME=[40151500:01C27606] This is a multi-part message in MIME format. --------------29E7F667DF923B42649B7D70 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit dear ccl, our research group has been running the gaussian 98 program on ibm rs/6000 machines. we have never had any problems with this system. we are now looking to buy a new system and have limited funds. it seems as though we can get alot more for our money if we buy a parallel quantum solutions machine type. my question is -- is this type of system compatible and reliable and a good choice for running large high end calculations using the gaussian 98 program ? any comments? -- Monica C. Concha Research Associate Dept. Of Chemistry University of New Orleans New Orleans LA 70148 E-mail mconcha@uno.edu --------------29E7F667DF923B42649B7D70 Content-Type: text/x-vcard; charset=us-ascii; name="mconcha.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for M—nica C. Concha Content-Disposition: attachment; filename="mconcha.vcf" begin:vcard n:Concha;Monica C. tel;fax:504-280-6860 tel;home:504- 456-2325 tel;work:504-280-7216 x-mozilla-html:FALSE org:University of New Orleans;Chemistry adr:;;Lakeshore;New Orleans;LA;70148;USA version:2.1 email;internet:mconcha@uno.edu title:Research Associate x-mozilla-cpt:;1 fn:Monica C. Concha end:vcard --------------29E7F667DF923B42649B7D70-- From chemistry-request@server.ccl.net Thu Oct 17 15:04:22 2002 Received: from mmp-1.mssm.edu ([146.203.100.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HJ4Lf32079 for ; Thu, 17 Oct 2002 15:04:22 -0400 Received: from CONVERSION-DAEMON.mmp-1.mssm.edu by mmp-1.mssm.edu (PMDF V6.1 #38773) id <0H45007013N8D0@mmp-1.mssm.edu> for chemistry@ccl.net; Thu, 17 Oct 2002 15:04:22 -0400 (EDT) Received: from SANDHYAPRECISION340 ([146.203.3.168]) by mmp-1.mssm.edu (PMDF V6.1 #38773) with SMTP id <0H45006F93N8OJ@mmp-1.mssm.edu> for chemistry@ccl.net; Thu, 17 Oct 2002 15:04:20 -0400 (EDT) Date: Thu, 17 Oct 2002 15:03:30 -0400 From: Sandhya Subject: charmm topology and parameters To: chemistry@ccl.net Message-id: <001801c2760f$e1e47cf0$a803cb92@SANDHYAPRECISION340> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 X-Mailer: Microsoft Outlook Express 5.50.4807.1700 Content-type: multipart/alternative; boundary="Boundary_(ID_4sN4Y0dtM7S3Q9t64bNe8g)" X-Priority: 3 X-MSMail-priority: Normal This is a multi-part message in MIME format. --Boundary_(ID_4sN4Y0dtM7S3Q9t64bNe8g) Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: quoted-printable Hi all, I am trying to fix topology and parameters for ligands typically with 7 = membered rings. Could anybody help me with charmm atom types for = Nitrogen and Carbon in a seven membered ring. Thanking you in advance. Sandhya Department of Physiology & Biophysics, Box 1218 Mount Sinai School of Medicine One Gustave L Levy Place, New York, 10029 NY Ph: 212-2411611 kortagere.sandhya@mssm.edu= --Boundary_(ID_4sN4Y0dtM7S3Q9t64bNe8g) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE
Hi all,
I am trying to fix topology and para= meters for=20 ligands typically with 7 membered rings. Could anybody help me with c= harmm atom=20 types for Nitrogen and Carbon in a seven membered ring. Thanking you = in=20 advance.
 
Sandhya
Department of Physiology = &=20 Biophysics, Box 1218
Mount Sinai School of Medicine
One Gustave= L Levy=20 Place,
New York, 10029 NY
Ph: 212-2411611
kortagere.sandhya@mssm.edu=
--Boundary_(ID_4sN4Y0dtM7S3Q9t64bNe8g)-- From chemistry-request@server.ccl.net Thu Oct 17 14:09:32 2002 Received: from mail.med.cornell.edu ([140.251.3.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HI9Wf31069 for ; Thu, 17 Oct 2002 14:09:32 -0400 Received: from cornell.edu ([140.251.122.57]) by mail.med.cornell.edu (Netscape Messaging Server 3.6) with ESMTP id AAA84BA; Thu, 17 Oct 2002 14:09:10 -0400 Date: Thu, 17 Oct 2002 14:09:22 -0400 Subject: Re: CCL:Macintosh questions Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v546) Cc: chemistry@ccl.net To: Joe M Leonard From: Simon Berneche In-Reply-To: <200210151923.PAA02005@world.std.com> Message-Id: <90180ACF-E1FB-11D6-8508-0030653F9806@cornell.edu> Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.546) Joe, > 1) What is the large-scale/floating point performance between the > newest > Macs and Intel machines? Is there any particular compilers and/or > switches > needed to realize max performance? The G4 processor is not in a position to compete with Intel/AMD cpu for number crunching except if you can limit your calculation to single precision floating points. In that case you can use the G4's vectorial unit (Altivec) to bring the performance at the level of what Intel/AMD cpu would provide. > 2) How does OSX compare to Linux as a development environment? Can one > do C and Fortran coding (or more-modern languages) on these machines? > Are there particular problem areas? The same tools are available on both platforms. You can install all gnu stuff, including the X11 window server (and run simultaneously X11 and Apple's Aqua windowing systems). Apple's compiler is in fact gcc (they don't ship g77 with it, but it can easily be installed). If you do a lot of Fortran I would recommend buying one of the commercial compilers (Absoft has a good one). Python and perl are pre-installed, I think Ruby is also. Even if you don't need to use it, a lot of people seem to appreciate the Cocoa API and the Obj-C language (both are heritages of NextStep, the ancestor of MacOS X). > 3) Is there any problem giving presentations from a Mac rather than > a PC (both laptops)? Or, are the suitable video-out ports supported > on each? No problem at that level. Also, there is no chance that your slideshow application would bring the OS down in middle of a presentation. The app might crash, but it has a really low-low probability of affecting the OS, like it could have been the case with MacOS 9 or Windows. In two words, with MacOS X underneath, Macs are really good desktop/laptop UNIX machines with the bonus that you can also run mainstream applications like Photoshop and Office without rebooting in an other OS (Windows or MacOS 9) or switching to another machine. They are not that great for number crunching, but that could change rapidly in the coming year with the latest announcement of IBM PowerPC 970 chip. Hope this helps. Simon ____________________________________________ Simon BERNECHE B.R. Theoretical Biophysics Laboratory Weill Medical College of Cornell University email: simon.berneche@cornell.edu tel:(212)746-4237 fax: (212)746-4843 ____________________________________________ From chemistry-request@server.ccl.net Fri Oct 18 03:13:42 2002 Received: from laplinux.dcfe.unimi.it ([159.149.31.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9I7Dgi22050 for ; Fri, 18 Oct 2002 03:13:42 -0400 Received: from laplinux.dcfe.unimi.it (localhost [127.0.0.1]) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/SuSE Linux 0.6) with ESMTP id g9I7DGmY018655; Fri, 18 Oct 2002 09:13:16 +0200 Received: from localhost (acontini@localhost) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/Submit) with ESMTP id g9I7DGI4018652; Fri, 18 Oct 2002 09:13:16 +0200 X-Authentication-Warning: laplinux.dcfe.unimi.it: acontini owned process doing -bs Date: Fri, 18 Oct 2002 09:13:16 +0200 (CEST) From: Alessandro Contini X-X-Sender: acontini@laplinux.dcfe.unimi.it To: Antoine Logean cc: chemistry@ccl.net Subject: Re: CCL:Amber 6 : from amber format to PDB with xleap In-Reply-To: <3DAEBA1B.6040203@pharma.u-strasbg.fr> 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 g9I7Dgi22051 Dear Antoine, first I'd like to salute you, I'm back in milan... Second: tou can yse the command: ambpdb -p file.top -tit "TITLE" -bres < file.xyz > file.pdb if you want to get the pdb file from the optimized coordinates. An alternative is to use the command ptraj file.top < ptraj.in where ptraj.in is a little script where you specify various options: Example: you want to get the pdb file from the restart coordinates of an amber run of the "enzyme" file, but you dont want box info in it and you want to remove all water molecules; so you have to digit: ptraj enzyme.top < ptraj.in where ptraj.in contains the following lines: trajin enzyme.rst 1 1 trajout enzyme.pdb pdb nowat strip :WAT go Ciao Alessandro Contini Dott. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm On Thu, 17 Oct 2002, Antoine Logean wrote: > Dear all, > Dear Amber users, > > My problem is the following : > > In xleap I prepare the input file for sander : > > model = loadPDB X.pdb > saveAmberParm model X.topol X.xyz > quit > > and I start the minimization with sander : > > sander -i min.in -o min.out -p X.topol -c X.xyz -r X.minxyz > > OK all work fine. My question is know by using xleap how can > I convert X.minxyz (the sander output in the amber format) in > a standart PDB file ? (the equivalent of pdbgen in the previous > version) > > Thank you for your help. > > Antoine > > > -= 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 Oct 18 03:57:38 2002 Received: from gatekeeper.itqb.unl.pt ([193.136.177.1]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g9I7vai23229 for ; Fri, 18 Oct 2002 03:57:37 -0400 Received: (qmail 31509 invoked from network); 18 Oct 2002 07:57:24 -0000 Received: from mistral.itqb.unl.pt (herrmann@193.136.176.14) by gatekeeper.itqb.unl.pt with SMTP; 18 Oct 2002 07:57:24 -0000 Received: from localhost (herrmann@localhost) by mistral.itqb.unl.pt (8.9.3/8.9.3) with ESMTP id IAA27846 for ; Fri, 18 Oct 2002 08:57:24 +0100 Date: Fri, 18 Oct 2002 08:57:24 +0100 (WEST) From: Rudolf Herrmann To: chemistry@ccl.net Subject: Summary II: G98: VOVl3 problem: convergence criterion not met In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, since there arrived some more answers to my question after having submitted the summary, there is a second one. Thanks to Viswanathan Balakrishnan, Olga Dmitrenko, Stefan Konietz and N.Sukumar. R.Herrmann. My original question: --------------------------------------------------------------------------- Hello, I recently tried to calculate the NMR chemical shifts of VOCl3 with Gaussian 98: --------------------------------------- #B3LYP/6-31G* SP NMR VOCl3 0 1 cl cl 1 clcl2 cl 2 clcl3 1 clclcl3 o 3 ocl4 2 oclcl4 1 dih4 v 3 vcl5 2 vclcl5 1 dih5 clcl2 3.506363 clcl3 3.506243 clclcl3 59.999 oclcl4 53.376 dih4 -64.586 vcl5 2.118170 vclcl5 34.144 dih5 -31.640 -------------------------------- The result (even with several variations in the input) is always an error termination when trying the "incremental Fock formation" (convergence criterion not met). The structure was optimized with GAMESS. Any suggestion what I could do is wellcome - thank you! --------------------------------- 108 basis functions 288 primitive gaussians 41 alpha electrons 41 beta electrons nuclear repulsion energy 561.9817715949 Hartrees. One-electron integrals computed using PRISM. NBasis= 108 RedAO= T NBF= 108 NBsUse= 108 1.00D-04 NBFU= 108 Projected Huckel Guess. Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Virtual orbitals will be shifted by 0.200 hartree. Restarting incremental Fock formation. Restarting incremental Fock formation. Restarting incremental Fock formation. >>>>>>>>>> Convergence criterion not met. SCF Done: E(RB+HF-LYP) = -2359.59549049 A.U. after 65 cycles Convg = 0.5851D-03 -V/T = 1.9657 S**2 = 0.0000 Convergence failure -- run terminated. Error termination via Lnk1e in /usr/local/g98_a7/l502.exe. Job cpu time: 0 days 0 hours 16 minutes 33.0 seconds. File lengths (MBytes): RWF= 14 Int= 0 D2E= 0 Chk= 1 Scr= 1 -------------------------------------------------------------------------- The new answers: 1. From: Viswanathan Balakrishnan To: Rudolf Herrmann Subject: Re: CCL:G98: VOCl3 problem: convergence criterion not met Dr. Hermann, I tried out the input file which you had supplied to CCL and noticed that I was able to run the job to normal termination using scf=qc keyword. Balakrishnan --------------------------------------------------------------------------- 2. From: Olga Dmitrenko To: herrmann@itqb.unl.pt Subject: VOCl3 question Dear Dr. Herrmann, In responce to your question posted on ccl, I would suggest you either to do first job with different basis set (try for instance, lanl2mb) and in the next step read wavefunction (guess=read), or use in your job options scf(maxcyc=300) scfcon=6 or even 5. When you get convergence, re-do with default criteria. Best regards, Olga --------------------------------------------------------------------------- 3.Dear Dr.Herrmann, Here is another suggestion from my friend: he needs to use Vshift, QC definitely. This is the only condition when my problem converged (I had a similar problem). Something like # b3lyp/6-31G* NMR Integral(FineGrid) scf(Vshift, QC) should work. Best regards, Olga Dmitrenko ---------------------------------------------------------------------------- 4. From: konietz@uni-duesseldorf.de To: Rudolf Herrmann Subject: Re: CCL:G98: VOCl3 problem: convergence criterion not met Dear Rudolf, try scf(maxcycle=300) and look what happens. I dont know how familiar you are with NMR calcs, if you are and your input is just a test input, stop reading here otherwise consider the following. You should use better basis sets than 6-31G* try 6-31+G(2df) or something similar. I dont know wether this is available for Vanadium or not. Use the tight option for the scf keyword. If you like to calculate chemical shifts, the geometry optimization of the standard and the system of interest should be on the same level of theory. The NMR calcs should be on a very high level (basis) but also on the same level for the standard and the investigated system. Have fun, Stefan. ------------------------------------------------------------------------- 5. From: Dr. N. SUKUMAR To: herrmann@itqb.unl.pt Subject: Re: CCL:G98: VOCl3 problem: convergence criterion not met Parts/Attachments: 1 Shown ~3.5 KB Text 2 29 KB Application 3 574 KB Application ---------------------------------------- Worked for me as a composite job: %nproc=2 %chk=vocl3.chk #HF/6-31G* SCF=Sleazy VOCl3 0 1 cl cl 1 clcl2 cl 2 clcl3 1 clclcl3 o 3 ocl4 2 oclcl4 1 dih4 v 3 vcl5 2 vclcl5 1 dih5 clcl2 3.506363 clcl3 3.506243 clclcl3 59.999 ocl4 2.938735 oclcl4 53.376 dih4 -64.586 vcl5 2.118170 vclcl5 34.144 dih5 -31.640 -- Link1 -- %nproc=2 %chk=vocl3.chk #B3LYP/6-31G* SP NMR Geom=CheckPoint Guess=Read VOCl3 0 1 Log and gzipped checkpoint files attached. Dr. N. Sukumar ------------------------------------------------------------------------- (Attachments not included in the summary) R.H. -- Dr. Rudolf Herrmann Instituto de Tecnologia Quimica e Biologica (ITQB) Av. da Republica, EAN, Apt. 127 P-2781-901 Oeiras e-mail: herrmann@itqb.unl.pt From chemistry-request@server.ccl.net Thu Oct 17 16:57:09 2002 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HKv9f01590 for ; Thu, 17 Oct 2002 16:57:09 -0400 Received: from daveg.cachesoftware.com ([192.168.110.100]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id g9HKv7t25657; Thu, 17 Oct 2002 13:57:07 -0700 Message-Id: <5.1.0.14.0.20021017131715.037fa1e0@pop3.norton.antivirus> X-Sender: daveg/mail.cachesoftware.com@pop3.norton.antivirus X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 17 Oct 2002 13:56:15 -0700 To: Rami Reddy From: David Gallagher Subject: Re: CCL:Computer programs for estimating pKa values of small values Cc: chemistry@ccl.net In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed To get the highest accuracy for your particular compounds, you can compute pKa using a quantitative structure-property relationship (QSPR) calibrated with some examples from your classes of compounds. One of the fastest QSPR methods uses the partial charge (from a MOPAC AM1 calculation) of the acidic proton. The calculations would take from a few seconds to a few minutes each on a Pentium-III based system. The CAChe Worksystem package automates these calculations and much of the QSPR set up. There is an application note on predicting pKa at http://www.cachesoftware.com/pdfs/EstpKa.pdf and a multimedia movie about QSPR&QSAR at http://www.cachesoftware.com/movies/QSARMovie.exe An alternative but slower method is to compute free energy of de-protonation. David Gallagher, CAChe Group, Fujitsu. At 09:42 AM 10/17/2002 -0700, Rami Reddy wrote: >We are looking for a computer program for estimating pKa values of small >molecules (MW<500). If you know any good computer program(s), please let me >know ASAP with all the details. > >Thanks, >M. Rami Reddy >Tel: (858)-622-3967 >Emal: reddy@mbasis.com > >-= 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 ============================================== David A. Gallagher, C. Chem. Vice President, Sales and Marketing CAChe Group Fujitsu America, Inc. 15244 NW Greenbrier Parkway Beaverton, OR 97006-5733, USA Direct dial: 503 746 3607 Main Switchboard: 503 746 3600 Fax: 503 531 9966 email: dgallagher@cachesoftware.com URL: http://www.cachesoftware.com ============================================== From chemistry-request@server.ccl.net Thu Oct 17 14:36:57 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9HIavf31644 for ; Thu, 17 Oct 2002 14:36:57 -0400 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id OAA12100; Thu, 17 Oct 2002 14:36:56 -0400 (EDT) Sender: richard@cornell.edu Message-ID: <3DAF0348.9838B40C@cornell.edu> Date: Thu, 17 Oct 2002 14:36:56 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: Joe M Leonard CC: chemistry@ccl.net Subject: Re: CCL:Macintosh questions References: <200210151923.PAA02005@world.std.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Joe M Leonard wrote: Joe: I use RH Linux at work running on a 1GHz AMD but use MacOS X (Jaguar) at home on an older 400Mhz G4. When I upgrade my box at work I will choose Mac. Not so much because G4's are faster, but because the system is so nice to work with and finally has all the tools I need. > I would welcome any guidance on the following questions (and > assume somebody reading this has played with new Macintoshes): > > 1) What is the large-scale/floating point performance between the newest > Macs and Intel machines? Is there any particular compilers and/or switches > needed to realize max performance? I have not run any serious benchmarks. I'll do a quicky tonight just out of curiosity. Disk access seems to be quite a bit faster than the IDE disk I'm currently using under Linux. The default compiler is gcc. I did skim though the compiler manual ... there are examples and the syntax is pretty simple. You need to recode loops to take advantage of the pipeline. At the present time, I don't consider it worth optimizing code since I don't run many production jobs at home. We are still building another large diskless Linux cluster for production work here at MacCHESS. Cost is the main consideration there. You can run MPI accross multiple G4's of course. Michael Love in our group does a lot of that. > 2) How does OSX compare to Linux as a development environment? Can one > do C and Fortran coding (or more-modern languages) on these machines? > Are there particular problem areas? Apple has a very very nice development environment ... all comes free with Jaguar (even a version of Python is installed by default). Just double click on a source code file and it will launch the Project Builder (http://developer.apple.com/tools/projectbuilder/). I use it mainly as an editor, but it is something like Dev Studio in the M$ world only for gnu compilers. I wish they had a Linux version for work. Yes you can get FORTRAN (at least g77, probably others by now). Essentially all Linux/Unix apps have been ported. You can check out www.gnu-darwin.org or http://fink.sourceforge.net/ to see what all is available. With XDarwin, you can run X-windows apps on your Jaguar desktop, (I run OpenDX, gnuplot and xv this way). or simply run Darwin with XFree86 and have the box look just like anyother Linux or BSD. > > 3) Is there any problem giving presentations from a Mac rather than > a PC (both laptops)? Or, are the suitable video-out ports supported > on each? As far as I know (I don't own a laptop). I use PowerPoint for the Mac and just burn a CD that will run work on either type machine. Richard > > Thanks in advance! > > Joe Leonard > jle@theworld.com > > P.S. I figure our audience is sufficiently different to make "typical reviews" > less than valuable :-). > > -= 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 Oct 18 19:37:56 2002 Received: from GoCovista.com ([12.227.131.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9INbti15624 for ; Fri, 18 Oct 2002 19:37:55 -0400 Message-Id: <200210182337.g9INbti15624@server.ccl.net> From: Nate@GoCovista.com To: chemistry@ccl.net Subject: One dozen 12oz. to 16oz. Idaho Potatoes Date: 18 Oct 2002 17:38:19 -0600 MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 8bit Most people think a big Idaho Potato on a good day is about as big as a lady's fist. They can be 3 to 6 times that big! Americans never see Idaho's best potatoes. They're made into french fries. These "bakers" are humongous. Potatoes are about the most inexpensive food you can buy...especially when you consider their impressive food value. The next time you serve a special dinner or entertain guests, you can really wow them with these 10 inch long beauties. Please indicate your interest by responding to this email address...and if you'd be interested in 50 lbs of Idaho's best potatoes shipped to you every 2 to 4 months, let us know. New Millennium/TIPS Nate@GoCovista.com From chemistry-request@server.ccl.net Fri Oct 18 16:43:42 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9IKhgi09052 for ; Fri, 18 Oct 2002 16:43:42 -0400 Received: from cornell.edu (dopey.lassp.cornell.edu [128.84.241.121]) by cornell.edu (8.9.3/8.9.3) with ESMTP id QAA05383 for ; Fri, 18 Oct 2002 16:43:41 -0400 (EDT) Message-ID: <3DB0727E.73E0B0AC@cornell.edu> Date: Fri, 18 Oct 2002 16:43:42 -0400 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Gaussian error message?? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi -- Thanks for the earlier replies to my Gaussian questions. This list and the people on it have been so helpful... I fixed the memory usage problem (I think), but I'm getting another error message I was hoping someone could help me decipher: What does Connecting fragments in GConA failed mean? Thanks, Connie %mem=800mb %rwf=T:\cc236\temp1.rwf,280MW,T:\cc236\temp2.rwf,280MW,T:\cc236\temp3.rwf,-1 -------------- # PM3 Opt Test -------------- 1/14=-1,18=50,19=11,26=3,38=1/1,3; 2/9=110,17=6,18=5,40=1/2; 3/5=2,11=9,12=1,25=1,30=1/1; 4/5=3,11=1,20=7,22=1,24=1,35=1/1,2; 6/7=2,8=2,9=2,10=2/1; 7//16; 1/14=-1,18=50,19=11/3(1); 99//99; 2/9=110/2; 3/5=2,11=9,12=1,25=1,30=1/1; 4/5=5,11=1,16=2,20=7,22=1,24=1,35=1/1,2; 7//16; 1/14=-1,18=50,19=11/3(-4); 2/9=110/2; 6/7=2,8=2,9=2,10=2/1; 99//99; ------------------ No title specified ------------------ Symbolic Z-matrix: Charge = 0 Multiplicity = 1 Connecting fragments in GConA failed. Error termination via Lnk1e in l101.exe. Job cpu time: 0 days 0 hours 0 minutes 2.0 seconds. File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1 From chemistry-request@server.ccl.net Fri Oct 18 14:44:55 2002 Received: from mum.mans.edu.eg ([193.227.50.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9IIiri07390 for ; Fri, 18 Oct 2002 14:44:54 -0400 Received: by mum.mans.edu.eg with Internet Mail Service (5.5.2656.59) id <49FSQ0H1>; Fri, 18 Oct 2002 20:47:05 +0200 Message-ID: <4C7A402190F4BD4385075D6B739AB4141394F9@mum.mans.edu.eg> From: Tarek Mamoun El-Gogary To: "'CHEMISTRY@ccl.net'" Subject: solvent cutoff wavelength Date: Fri, 18 Oct 2002 20:46:58 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: text/plain Dear CCL members, I am sorry to post this general question. I am using a double beam spectrophotometer to measure the electronic absorption spectra of some organic compounds, so I am using the solvent as a blank and run autozeroing before scanning the sample. My question is: should I stop scanning at the cutoff wavelength (240 nm) of the solvent or may I measure the samble beyond the cutoff wavelength of the solvent? As the solvent is in the blank cell so its interference will be eliminated, is that correct? regards Tarek