From chemistry-request@ccl.net Fri Jul 1 13:50:45 2005 Received: from smtp1.Stanford.EDU (smtp1.Stanford.EDU [171.67.16.123]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j61HoaYx018985 for ; Fri, 1 Jul 2005 13:50:37 -0400 Received: from cardinal1.Stanford.EDU (cardinal1.Stanford.EDU [171.64.15.249]) by smtp1.Stanford.EDU (8.12.11/8.12.11) with ESMTP id j61HoXEl013043 for ; Fri, 1 Jul 2005 10:50:33 -0700 Date: Fri, 1 Jul 2005 10:50:33 -0700 (PDT) From: "S.I.Gorelsky" To: chemistry !! ccl.net Subject: Re: CCL:dual-core Opteron 275 performance In-Reply-To: <6.1.2.0.2.20050701083953.032f5480 !! po.chem.ucla.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net I am sure, we all will be glad to hear about this "valid" comparison. So far, I have not seen any reports on the performance of dual-core dual-CPU Xeon servers. Thus, I am reporting the data I got by running the machines that are available to me. If you have the dual-core dual-CPU Xeon data, please post! Then, everyone will decide for him/herself what's faster/better/cheaper. Regards, s.g. > A valid comparison is dual-core dual-CPU Opteron 275 workstation versus > dual-core dual-CPU Xeon 3.X GHz workstation. > > > > At 11:00 PM 6/30/2005, you wrote: > > >To add to the discussion about the performance of new dual-core > >processors for computational chemistry applications, > > > >the comparison of Intel and AMD dual-CPU based computers is shown at: > > > >http://www.sg-chem.net/cluster/ > > > >As can be seen from the graph, the Gaussian 03 execution speed (test job > >397) on dual-core dual-CPU Opteron 275 workstation is faster by a factor > >of 1.95 > >as compared to the dual-CPU Xeon 3.2GHz 800MHz FSB machine. > > > >----------------- > > > >I would like to thank Ed Gasiorowski (AMD) and Mike Fay (Colfax > >International) for their support. > > > >Serge Gorelsky > > > >---------------------------------------------------------------- > > Dr S.I. Gorelsky, Department of Chemistry, Stanford University > > Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA > > Phone: (650) 723-0041. Fax: (650) 723-0852. > >---------------------------------------------------------------- > > > > > > > > > > > > > > > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST !! ccl.net > >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > > >use the Web based form from CCL Home Page > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY !! ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST !! ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0852. ---------------------------------------------------------------- From chemistry-request@ccl.net Fri Jul 1 22:55:43 2005 Received: from rproxy.gmail.com (rproxy.gmail.com [64.233.170.201]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j622tbFd012487 for ; Fri, 1 Jul 2005 22:55:37 -0400 Received: by rproxy.gmail.com with SMTP id a41so350654rng for ; Fri, 01 Jul 2005 19:55:36 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:date:to:subject:references:from:content-type:mime-version:content-transfer-encoding:message-id:in-reply-to:user-agent; b=iBzOFy4sLh4D0ajEJ2VDOF5PAd5+e6qktSPtzdnnDgzKcpLVosArE5yFODfGbFrUhib1O5vP8OEbX/PDYo5qJdR2tqQf2P3mAgtwJZPb8o3a2YuJBqjcL/5GAumdnrLuvEAE5toojzVdwwpaOTBRpTHbG4+vmp8iDCj8U87PZwM= Received: by 10.38.98.62 with SMTP id v62mr1259767rnb; Fri, 01 Jul 2005 18:55:25 -0700 (PDT) Received: from qcmm9 ([61.183.207.53]) by mx.gmail.com with ESMTP id c3sm443516rne.2005.07.01.18.55.24; Fri, 01 Jul 2005 18:55:25 -0700 (PDT) Date: Sat, 02 Jul 2005 09:53:59 +0800 To: chemistry !! ccl.net Subject: Re: CCL:SUMARRY --- 3D->2D softwares? References: <20050618225857.40395.qmail !! web41201.mail.yahoo.com> From: "JunJun Liu" Content-Type: text/plain; format=flowed; delsp=yes; charset=utf-8 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-ID: In-Reply-To: User-Agent: Opera M2(BETA3)/8.0 (Linux, build 1019) X-Spam-Status: No, score=0.5 required=5.0 tests=FROM_ENDS_IN_NUMS,RCVD_BY_IP autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Deal All: After receiving Ogham academic licenses now, I can evaluate all the recommended programs. Thanks all that gave me advices! I have a lot of molecules to be converted to 2D images, so a command line program is more of interest. Among the below recommended softwares, I like MolConverter and Ogham most, although these two programs still have some shortcomes. Molconverter: 1. works well only when remove all hydrogens. 2. it has some problem in recognizing some aromatic rings. Ogham: 1. works a slightly better and smarter, but the program could be used for only two months with an academic license. 2. the produced images will be stamped with an OpenEye logo. ----- Recommended Softwares ------- MolConverter (in the package of Marvin) http://www.chemaxon.hu/marvin/ JChemPaint http://jchempaint.sf.net/ Ogham one product of OpenEye Scientific Softwares. http://www.eyesopen.com/products/toolkits/ogham.html xdrawchem http://xdrawchem.sourceforge.net/ CACTVS http://www.xemistry.com ------------------------------ Best Regards! Liu On Mon, 27 Jun 2005 15:56:15 +0800, JunJun Liu wrote: > Dear All: > > Is there a software in linux can convert 3D small organic structures to > 2D > sketch structures? It will be more preferable if the software has a > function of exporting 2D structures to picutures. Thanks in advance! > > Liu > > -- JunJun Liu College of Chemistry Central China Normal University WuHan 430079 P.R. China From chemistry-request@ccl.net Fri Jul 1 16:37:18 2005 Received: from exmails1.chem.ucla.edu (exmails1.chem.ucla.edu [169.232.134.2]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j61KbBIR026962 for ; Fri, 1 Jul 2005 16:37:12 -0400 Received: from chem.ucla.edu (d-128-97-138-86.chem.ucla.edu [128.97.138.86]) by exmails1.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id j61KaxKe006404; Fri, 1 Jul 2005 13:36:59 -0700 Date: Fri, 1 Jul 2005 13:36:46 -0700 Subject: philosophy of chemistry conference, this August Content-Type: multipart/alternative; boundary=Apple-Mail-47-209085944 Mime-Version: 1.0 (Apple Message framework v553) Cc: philchem philchem , CCL , hopos , hist !! exmails1.chem.ucla.edu To: chemed chemed From: Eric Scerri Message-Id: X-Mailer: Apple Mail (2.553) X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net --Apple-Mail-47-209085944 Content-Transfer-Encoding: 7bit Content-Type: text/plain; delsp=yes; charset=US-ASCII; format=flowed The International Society for the Philosophy of Chemistry, ISPC, http://ispc.sas.upenn.edu/ will hold its next meeting from August 7-11th at the University of Tennesse at Knoxville, TN, USA. Details from Professor Jeffrey Kovac, jkovac !! utk.edu See web pages below for further details of publications, official journal and society, Dr. Eric Scerri, Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA 90095- 1569 E-mail scerri !! chem.ucla.edu Tel: 310 206 7443 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.springeronline.com/sgw/cda/frontpage/0,11855,4-0-70- 35545882-0,00.html?referer=www.wkap.nl Also see International Society for the Philosophy of Chemistry http://ispc.sas.upenn.edu/ --Apple-Mail-47-209085944 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Courier New2020,2020,2020The International Society for the Philosophy of Chemistry, ISPC, 2424,7C7C,D4D4http://ispc.sas.upenn.edu/2020,2020,2020 will hold its next meeting from August 7-11th at the University of Tennesse at Knoxville, TN, USA. Details from Professor Jeffrey Kovac, jkovac !! utk.edu2020,2020,2020 See web pages below for further details of publications, official journal and society, Dr. Eric Scerri, Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA 90095- 1569 E-mail scerri !! chem.ucla.edu Tel: 310 206 7443 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.springeronline.com/sgw/cda/frontpage/0,11855,4-0-70-35545882-0,00.html?referer=www.wkap.nl Also see International Society for the Philosophy of Chemistry http://ispc.sas.upenn.edu/ --Apple-Mail-47-209085944-- From chemistry-request@ccl.net Fri Jul 1 13:59:45 2005 Received: from authusersmtp.mail.cornell.edu (granite1.mail.cornell.edu [128.253.83.141]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j61HxatV019372 for ; Fri, 1 Jul 2005 13:59:37 -0400 Received: from [192.168.0.139] (abruna-gw1.chem.cornell.edu [128.253.34.140]) (authenticated bits=0) by authusersmtp.mail.cornell.edu (8.13.1/8.12.10) with ESMTP id j61I3LNH012258 (version=TLSv1/SSLv3 cipher=RC4-SHA bits=128 verify=NOT) for ; Fri, 1 Jul 2005 14:03:22 -0400 (EDT) Mime-Version: 1.0 (Apple Message framework v730) In-Reply-To: <42C55A9D.2040604 +*+ pobox.com> References: <42C55A9D.2040604 +*+ pobox.com> Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Message-Id: From: Geoff Hutchison Subject: Re: CCL:Two Questions about finding code Date: Fri, 1 Jul 2005 13:59:34 -0400 To: chemistry +*+ ccl.net X-Mailer: Apple Mail (2.730) X-Spam-Status: No, score=0.5 required=5.0 tests=FROM_ENDS_IN_NUMS autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j61HxjtV019377 > 1) Can anyone recommend a good source for code that can calculate > various molecular descriptors (a la QSAR/QSPR use)? Open Source would > be really nice Well, off the top of my head, I can think of several open source packages (part of the Blue Obelisk movement) JOELib:http://www-ra.informatik.uni-tuebingen.de/software/joelib/ Octet:http://octetsource.net/ QSAR:http://qsar.sourceforge.net/ There's also the Chemical Descriptors Library (CDL) though I haven't checked it in a while: CDL: http://cdelib.sourceforge.net/ > 2) Has anyone got any knowledge of the python bindings for > openbabel? Funny you should ask. Of course there is a mailing list for openbabel (openbabel-discuss @ lists.sourceforge.net) where there's been discussion about this in the past 6 weeks or so. There's even a new mailing list just for scripting language access to OpenBabel too. Long story short. I've been working more on the core API and the C++ code, but hacked up both Perl and Python wrappers. They do seem to work -- I'd be glad to continue the conversation off-list, since they're still development code and need testing. You have been warned. Source for Open Babel can be found through the website (the Perl and Python bits are in the 2005-07-01 development snapshot): http://openbabel.sourceforge.net/ http://sourceforge.net/projects/openbabel/ Cheers, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruqa Group http://abruna.chem.cornell.edu/ From chemistry-request@ccl.net Fri Jul 1 14:44:33 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j61IiWoK021770 for ; Fri, 1 Jul 2005 14:44:32 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j61IiWcD021769 for chemistry +*+ ccl.net; Fri, 1 Jul 2005 14:44:32 -0400 Date: Fri, 1 Jul 2005 14:44:32 -0400 Message-Id: <200507011844.j61IiWcD021769 +*+ server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request +*+ ccl.net using -f From: "Ruben, , Venegas" To: chemistry +*+ ccl.net X-Web-Message-Number: 050701144404-21739 Subject: W:Log D Predictions- Software X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hello Everyone: Can anybody recommend software for predicting Log D values? Im aware of the ACDLabs software. I just want to know if there are other options. I want to be able of running on batch mode and hopefully on a Linux box. Thanks in advance. Ruben From chemistry-request@ccl.net Fri Jul 1 15:50:10 2005 Received: from trentu.ca (mxbob.trentu.ca [192.75.12.131]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j61Jo1h0024851 for ; Fri, 1 Jul 2005 15:50:05 -0400 Received: (qmail 17685 invoked by uid 510); 1 Jul 2005 19:49:55 -0000 Received: from 209.42.102.117 by mxbob (envelope-from , uid 502) with qmail-scanner-1.24 (fsecure: 4.52/2461/libra database 2005-06-30/orion database 2005-06-29/avp(2005-06-30). spamassassin: 3.0.2. Clear:RC:1(209.42.102.117):. Processed in 0.038634 secs); 01 Jul 2005 19:49:55 -0000 X-Qmail-Scanner-Mail-From: elewars (a) trentu.ca via mxbob X-Qmail-Scanner: 1.24 (Clear:RC:1(209.42.102.117):. Processed in 0.038634 secs) Received: from unknown (HELO trentu.ca) (209.42.102.117) by trentu.ca with SMTP; 1 Jul 2005 19:49:55 -0000 Message-ID: <42C59DED.5030508 (a) trentu.ca> Date: Fri, 01 Jul 2005 15:47:57 -0400 From: errol lewars User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry (a) ccl.net Subject: Re: CCL:transition state, correction References: <320131914.03018 (a) nenu.edu.cn> <42C423C6.40003 (a) trentu.ca> In-Reply-To: <42C423C6.40003 (a) trentu.ca> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=1.2 required=5.0 tests=DEAR_SOMETHING, DNS_FROM_RFC_ABUSE,FORGED_RCVD_HELO autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net For (1) that should have been, of course: (1) is the sum of the "raw" energy (electronic energy...) and the ZPE and by subtraction... EL ----- errol lewars wrote: > 2005 June 30 > > Hello, > > Gaussian gives enthalpy and Gibbs free energy when you do a frequency > calculation (which to be valid must be done using exactly the same > level as was used for the geometry optimization, for example HF/3-21G > for both). The values are printed right after the frequencies, e.g. > > Zero-point correction= 0.173654 > (Hartree/Particle) > Thermal correction to Energy= 0.199937 > Thermal correction to Enthalpy= 0.200882 > Thermal correction to Gibbs Free Energy= 0.117979 > Sum of electronic and zero-point Energies= -2156.346839 > Sum of electronic and thermal Energies= -2156.320555 > Sum of electronic and thermal Enthalpies= -2156.319611 > Sum of electronic and thermal Free Energies= -2156.402514 > > The values of interest to you are probably > (1) Sum of electronic and zero-point Energies, > (2) Sum of electronic and thermal Enthalpies, > (3) Sum of electronic and thermal Free Energies > > (1) is the sum of the "raw" energy (electronic energy + internuclear > repulsion, best located at the end of an optimization just before > "RSMD", e.g.: > HF =-2156.520493|RMSD=1.429e-009...) and by subtraction from other > (1)-type values gives 0 K enthalpy differences (since at 0 K S = 0). > (2) is the enthalpy at 298.15 K and 1.0000 atmosphere ("room > temperature and pressure") . Subtraction from other (2)-type values > gives enthalpy differences at room temperature/pressure. > (3) is analogous to (2); substitute "Gibbs free energy" for "enthalpy". > > Look at the relevant Gaussian White Paper on their website. > > As for the Hessian of a transition state, I suppose you want to see if > this has one negative eigenvalue; so just ask Gaussian to calculate > the frequencies (I assume you have the optimized TS; that's another > problem) and see if there is exactly one imaginary vibrational freq. > > EL > ===== > > QnUqDH wrote: > >> Dear sir: >> I have two questions to ask you. first,how can we get enthalpy and >> Gibbs >> free energy from the output file of frequence calculation. sencond, >> how to >> caculate Hessian in finding transition state in Gaussian 98. >> >> >> > = This is automatically added to each message by the mailing script =- > >> >> >> >> >> >> >> >> >> > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY (a) ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST (a) ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Sat Jul 2 03:03:31 2005 Received: from rproxy.gmail.com (rproxy.gmail.com [64.233.170.192]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j6273SUu024682 for ; Sat, 2 Jul 2005 03:03:28 -0400 Received: by rproxy.gmail.com with SMTP id f1so353303rne for ; Sat, 02 Jul 2005 00:03:28 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:mime-version:content-transfer-encoding:message-id:content-type:to:from:subject:date:x-mailer; b=sUC+vY4S37SBPGYua9mCnxqrWVgUznoc4skQ5UYiWWrFaW+NTA+Gd7wMyHvm97+K/QT0ZuOGDdaYwh1J1h1QNxF9o7zEdbx3mhOKaFkG1asubMpZ5wd/NiGIq9kQKQgDEy/WuPU84VcaibQM4y0KNnyW//gs8EZjQFhm410poVA= Received: by 10.38.98.60 with SMTP id v60mr1378966rnb; Fri, 01 Jul 2005 23:02:12 -0700 (PDT) Received: from ?192.168.1.4? ([67.168.47.62]) by mx.gmail.com with ESMTP id f3sm609972rne.2005.07.01.23.02.12; Fri, 01 Jul 2005 23:02:12 -0700 (PDT) Mime-Version: 1.0 (Apple Message framework v622) Content-Transfer-Encoding: 7bit Message-Id: <2b227339a7527f23748a41d85073a6c0 () gmail.com> Content-Type: text/plain; charset=US-ASCII; format=flowed To: chemistry () ccl.net From: Andri Arnaldsson Subject: Bader charge analysis from Gaussian Date: Fri, 1 Jul 2005 23:02:11 -0700 X-Mailer: Apple Mail (2.622) X-Spam-Status: No, score=0.0 required=5.0 tests=RCVD_BY_IP autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hello fellow CCL-ers, We have implemented and made freely available a grid based method to partition electron charge density according to Bader. A paper describing the method is currently in press in Computational Materials Science. Now Gaussian Cube files and VASP CHGCAR files can be read. A link to binaries, source code, and examples can be found at: http://theory.cm.utexas.edu/bader/ Questions can be directed to http://theory.cm.utexas.edu/forum/ Regards, Andri ----------------------------------------------------------------- Andri Arnaldsson Graduate Student Department of Chemistry, Box 351700 University of Washington Seattle, WA 98195-1700 Office: Bagley Hall, 311A Phone: (206)-543-7955 Email: andriuwashingtonedu URL: http://odinn.chem.washington.edu/~andri From chemistry-request@ccl.net Sat Jul 2 03:01:14 2005 Received: from rproxy.gmail.com (rproxy.gmail.com [64.233.170.202]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j62717jB024515 for ; Sat, 2 Jul 2005 03:01:07 -0400 Received: by rproxy.gmail.com with SMTP id f1so353139rne for ; Sat, 02 Jul 2005 00:01:06 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:mime-version:content-transfer-encoding:message-id:content-type:to:from:subject:date:x-mailer; b=nok9l/4Ajg3NDDZ6FNb/b44RSwKpltHcufUazuNpnOg+HFYAMgHq5kA/OV3M9ydT48gBXuxfwQIp9Q6X0ATMnfsYcq8Ld9+9nie3v8NrkrWxM0G4B1ZwQei0OV1w2YDckF4J8C2xei0Tg/DJl9QomBI5vWjYmPiIuMSKuY7T0nM= Received: by 10.38.67.39 with SMTP id p39mr1389020rna; Fri, 01 Jul 2005 23:02:11 -0700 (PDT) Received: from ?192.168.1.4? ([67.168.47.62]) by mx.gmail.com with ESMTP id f3sm609972rne.2005.07.01.23.02.10; Fri, 01 Jul 2005 23:02:11 -0700 (PDT) Mime-Version: 1.0 (Apple Message framework v622) Content-Transfer-Encoding: 7bit Message-Id: <9d88ea880d3212f4628bd6905eae2dad :: gmail.com> Content-Type: text/plain; charset=US-ASCII; format=flowed To: chemistry :: ccl.net From: Andri Arnaldsson Subject: Transition states with VASP Date: Fri, 1 Jul 2005 23:02:01 -0700 X-Mailer: Apple Mail (2.622) X-Spam-Status: No, score=0.0 required=5.0 tests=RCVD_BY_IP autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hello fellow CCL-ers We have been working on and made freely available extensions to VASP for finding transition states, minimum energy paths and dynamical (hessian) matrices. Source code, scripts for setting up calculations and extracting results can be found at: http://theory.cm.utexas.edu/vtsttools/ Questions can be directed to http://theory.cm.utexas.edu/forum/ Regards, Andri ----------------------------------------------------------------- Andri Arnaldsson Graduate Student Department of Chemistry, Box 351700 University of Washington Seattle, WA 98195-1700 Office: Bagley Hall, 311A Phone: (206)-543-7955 Email: andriuwashingtonedu URL: http://odinn.chem.washington.edu/~andri From chemistry-request@ccl.net Sat Jul 2 16:10:25 2005 Received: from chemaxon.hu (90.156-228-195.hosting.adatpark.hu [195.228.156.90]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j62KAHIf003771 for ; Sat, 2 Jul 2005 16:10:18 -0400 Received: from ktv32-66-73.catv-pool.axelero.hu ([62.201.73.66] helo=[192.168.0.3]) by chemaxon.hu with esmtpsa (Exim 4.44 #1 (Debian)) id 1DooJa-0001b9-G5 TLS Cipher TLSv1:AES256-SHA:256 for ; Sat, 02 Jul 2005 22:10:15 +0200 Message-ID: <42C6F48F.7040108 !=! chemaxon.com> Date: Sat, 02 Jul 2005 22:09:51 +0200 From: Ferenc Csizmadia User-Agent: Mozilla Thunderbird 1.0.2 (Windows/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry !=! ccl.net Subject: Re: CCL:SUMARRY --- 3D->2D softwares? References: <20050618225857.40395.qmail !=! web41201.mail.yahoo.com> In-Reply-To: Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Authenticated-Sender: 6b7f74379a61d7501896684c1ed90f1f X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Liu, Not sure what your specific issues were in the case of MolConverter, but I suggest to use our support for help: www.chemaxon.com/forum/ We may be able suggest some settings to improve the quality or to customize the image. Some comments about yours. There is no aromatic ring recognition at all if you use the default settings. If you want to see "aromatized" structures, you have to use some parameter settings. There are 3 related options: "a": level 1 aromatization "a_day": level 2 aromatization (more general than level 1) - "-a" dearomatization (Kekule representation instead of aromatic) Example: level 2 aromatization, 600x600 pixels, remove hydrogens molconvert png:a_dayw600-H input.mol >output.png I hope this helps. Best regards, Ferenc PS: The next version of JChem (and maybe Marvin) will support template-based 2D cleaning, so users will be able to define rules for the 2D representation. JunJun Liu wrote: > Deal All: > > After receiving Ogham academic licenses now, I can evaluate all the > recommended programs. Thanks all that gave me advices! I have a lot > of molecules to be converted to 2D images, so a command line program > is more of interest. Among the below recommended softwares, I like > MolConverter and Ogham most, although these two programs still have > some shortcomes. > Molconverter: > 1. works well only when remove all hydrogens. > 2. it has some problem in recognizing some aromatic rings. > > Ogham: > 1. works a slightly better and smarter, but the program could be used > for only two months with an academic license. > 2. the produced images will be stamped with an OpenEye logo. > > > ----- Recommended Softwares ------- > MolConverter (in the package of Marvin) > http://www.chemaxon.hu/marvin/ > > JChemPaint > http://jchempaint.sf.net/ > > Ogham > one product of OpenEye Scientific Softwares. > http://www.eyesopen.com/products/toolkits/ogham.html > > xdrawchem > http://xdrawchem.sourceforge.net/ > > CACTVS > http://www.xemistry.com > ------------------------------ > > Best Regards! > > Liu > > On Mon, 27 Jun 2005 15:56:15 +0800, JunJun Liu wrote: > >> Dear All: >> >> Is there a software in linux can convert 3D small organic structures >> to 2D >> sketch structures? It will be more preferable if the software has a >> function of exporting 2D structures to picutures. Thanks in advance! >> >> Liu >> >> > > From chemistry-request@ccl.net Sat Jul 2 18:11:48 2005 Received: from chemaxon.hu (90.156-228-195.hosting.adatpark.hu [195.228.156.90]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j62MBhvj018451 for ; Sat, 2 Jul 2005 18:11:45 -0400 Received: from 189.2-182-adsl-pool.axelero.hu ([81.182.2.189]) by chemaxon.hu with esmtpsa (Exim 4.44 #1 (Debian)) id 1DopTo-0003e3-Nm TLS Cipher TLSv1:AES256-SHA:256 for ; Sat, 02 Jul 2005 23:24:54 +0200 Message-ID: <42C70614.6020007:at:chemaxon.com> Date: Sat, 02 Jul 2005 23:24:36 +0200 From: Szabolcs Csepregi Organization: Chemaxon Ltd. User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry:at:ccl.net Subject: Re: CCL:W:Log D Predictions- Software References: <200507011844.j61IiWcD021769:at:server.ccl.net> In-Reply-To: <200507011844.j61IiWcD021769:at:server.ccl.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Authenticated-Sender: 6d9151da1e212c1b449e42f6a2f13dde X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Ruben, Marvin has a LogD plugin, which is also available from the batch program cxcalc: http://www.chemaxon.com/marvin/doc/user/calc.html Marvin is written in java, so it runs well on Linux. You can try marvin online at: http://www.chemaxon.com/demosite/marvin/index.html And the download page is: http://www.chemaxon.com/marvin/download.html Best regards, Szabolcs Ruben, , Venegas wrote: > Hello Everyone: > > Can anybody recommend software for predicting Log D values? > Im aware of the ACDLabs software. I just want to know if there are other options. > I want to be able of running on batch mode and hopefully on a Linux box. > > Thanks in advance. > > Ruben > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY:at:ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST:at:ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -- Szabolcs Csepregi, PhD Cheminformatics Scientist, ChemAxon Ltd. http://www.chemaxon.com Skype: szabolcs.csepregi Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659