From owner-chemistry@ccl.net Tue Nov 22 04:27:00 2005 From: "A. Rajendran raji|-|anal.chem.tohoku.ac.jp" To: CCL Subject: CCL:G: How to calculate the 31P NMR parameters using g03? Message-Id: <-30033-051122042449-9442-554A4mNhGfU5d+v3ygu7tA()server.ccl.net> X-Original-From: "A. Rajendran" Sent to CCL by: "A. Rajendran" [raji]^[anal.chem.tohoku.ac.jp] Dear CCL members, Could you please tell me how to calculate the 31P-NMR (as well Proton and 13C NMR) parameters/chemical shift values using gaussian03? Please send me a model input file and your explanation. Looking forward for your kind reply. You can also write to raji/at/anal.chem.tohoku.ac.jp Thanks in advance. Raj, Japan. From owner-chemistry@ccl.net Tue Nov 22 05:02:01 2005 From: "Pablo Vitoria pablo.vitoria(-)ehu.es" To: CCL Subject: CCL:G: [Fwd: W:Error with Frequency calculation when using genECP] Message-Id: <-30034-051122040611-2369-kEKcGUzu402Gqrw1BGsY8A++server.ccl.net> X-Original-From: "Pablo Vitoria" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Tue, 22 Nov 2005 09:26:42 +0100 MIME-Version: 1.0 Sent to CCL by: "Pablo Vitoria" [pablo.vitoria .. ehu.es] Hi, You should check that there is an empty line at the end of input file. Pablo ----- Original Message ----- > From: "don bunk bunk82 ~ newpaltz.edu" To: "Vitoria, Pablo " Sent: Sunday, November 20, 2005 5:35 AM Subject: CCL:G: [Fwd: W:Error with Frequency calculation when using genECP] > Sent to CCL by: "don bunk" [bunk82]-[newpaltz.edu] > This is a multi-part MIME message > > --_===28742318====newpaltz.edu===_ > Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" > Content-Transfer-Encoding: 8bit > > > > > --- the forwarded message follows --- > > --_===28742318====newpaltz.edu===_ > Content-Type: message/rfc822 > > X-ExtScanner: Niversoft's Find_Attachments > Return-Path: > Received: from rivendell.newpaltz.edu ([137.140.1.118] verified) > by newpaltz.edu (CommuniGate Pro SMTP 4.3.9) > with ESMTP id 28742056 for bunk82(_)newpaltz.edu; Sat, 19 Nov 2005 > 16:41:19 -0500 > Received: from rivendell.newpaltz.edu (localhost.localdomain [127.0.0.1]) > by localhost (Postfix) with SMTP id 719CAC38A > for ; Sat, 19 Nov 2005 16:41:18 -0500 (EST) > Received: from server.ccl.net (server.ccl.net [66.93.212.15]) > by rivendell.newpaltz.edu (Postfix) with ESMTP id 0AA32CF83 > for ; Sat, 19 Nov 2005 16:41:13 -0500 (EST) > Received: from server.ccl.net (ccl [127.0.0.1]) > by server.ccl.net (8.13.1/8.13.1) with ESMTP id jAJLf7ci019859 > for ; Sat, 19 Nov 2005 16:41:07 -0500 > Received: from 66.93.212.3 > (SquirrelMail authenticated user ccl) > by server.ccl.net with HTTP; > Sat, 19 Nov 2005 16:41:07 -0500 (EST) > Message-ID: <58303.66.93.212.3.1132436467.squirrel(_)server.ccl.net> > Date: Sat, 19 Nov 2005 16:41:07 -0500 (EST) > Subject: [Fwd: W:Error with Frequency calculation when using genECP] >> From: "Computational Chemistry List" > To: "Don Bunk" > Reply-To: ccl(_)ccl.net > User-Agent: SquirrelMail/1.4.6 [CVS]-0.cvs20050812.1.fc3 > MIME-Version: 1.0 > Content-Type: text/plain;charset=iso-8859-1 > X-Priority: 3 (Normal) > Importance: Normal > 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 > X-PMX-Version: 5.1.0.207369, Antispam-Engine: 2.1.0.0, Antispam-Data: > 2005.11.19.25 > X-PerlMx-Spam: Gauge=X, Probability=10%, Report='PRIORITY_NO_NAME 0.716, > __CT 0, __CTE 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0, __HAS_X_PRIORITY 0, > __MIME_TEXT_ONLY 0, __MIME_VERSION 0, __SANE_MSGID 0, __STOCK_CRUFT 0, > __USER_AGENT 0' > Content-Transfer-Encoding: quoted-printable > > Your message was not distributed to CCL Subscribers. > To send message to CCL subscribers you need to address it to > chemistry(_)ccl.net or choose Subscribers on the CCL Web Mailing form. > Jan > > ---------------------------- Original Message ---------------------------= > - > Subject: W:Error with Frequency calculation when using genECP >> From: "Don Bunk" > Date: Sat, November 19, 2005 4:36 pm > To: chemistry-request(_)ccl.net > -------------------------------------------------------------------------= > - > > Hey- > I'm trying to run a 3-stage job with two optimizations, one with, one wit= > h > out opt=3DZ-Matrix, and the third stage is a frequency calculation. It ge= > ts > hung upon the Effective core potentials on the frequency calculation > though. Any ideas? > My input file is as follows: > %chk=3Dhist_CdSH3.chk > %rwf=3D/scratch/hist_CdSH3.rwf > %int=3D/scratch/hist_CdSH3.int > %d2e=3D/scratch/hist_CdSH3.d2e > %nproc=3D2 > %mem=3D2gb > hf/genECP Opt=3D(NoEigen,Z-matrix,Maxcycle=3D999) > > Hist-CdSH3 hf Opt w/zm > > -2 1 > Cd1 > S2 1 R2 > H3 2 R3 1 A3 > S4 1 R4 2 A4 3 D4 > H5 4 R5 1 A5 2 D5 > S6 1 R6 2 A6 4 D6 > H7 6 R7 1 A7 4 D7 > N8 1 R8 2 A8 4 D8 > C9 8 R9 1 A9 4 D9 > C10 8 R10 1 A10 9 D10 > N11 10 R11 8 A11 9 D11 > C12 11 R12 10 A12 8 D12 > H13 10 R13 11 A13 8 D13 > H14 12 R14 11 A14 9 D14 > C15 9 R15 8 A15 12 D15 > H16 15 R16 9 A16 8 D16 > H17 15 R17 9 A17 16 D17 > C18 15 R18 9 A18 16 D18 > H19 18 R19 15 A19 16 D19 > N20 18 R20 15 A20 19 D20 > C21 18 R21 15 A21 19 D21 > H22 20 R22 18 A22 19 D22 > H23 20 R23 18 A23 22 D23 > O24 21 R24 18 A24 19 D24 > O25 21 R25 18 A25 24 D25 > H26 25 R26 21 A26 24 D26 > Variables: > R2=3D2.65768 > R3=3D1.33454 > R4=3D2.65770 > R5=3D1.33454 > R6=3D2.65767 > R7=3D1.33454 > R8=3D2.65771 > R9=3D1.37591 > R10=3D1.35137 > R11=3D1.28719 > R12=3D1.37209 > R13=3D1.07087 > R14=3D1.07107 > R15=3D1.49560 > R16=3D1.08480 > R17=3D1.08422 > R18=3D1.54307 > R19=3D1.08579 > R20=3D1.45391 > R21=3D1.52926 > R22=3D1.00205 > R23=3D1.00184 > R24=3D1.18563 > R25=3D1.31873 > R26=3D0.95650 > A3=3D96.379 > A4=3D105.494 > A5=3D96.386 > A6=3D105.516 > A7=3D96.384 > A8=3D117.734 > A9=3D126.590 > A10=3D126.197 > A11=3D112.194 > A12=3D105.200 > A13=3D125.656 > A14=3D121.331 > A15=3D123.158 > A16=3D108.601 > A17=3D110.562 > A18=3D113.316 > A19=3D108.766 > A20=3D110.626 > A21=3D107.868 > A22=3D111.477 > A23=3D111.181 > A24=3D107.661 > A25=3D117.018 > A26=3D108.496 > D4=3D159.635 > D5=3D-34.094 > D6=3D-125.331 > D7=3D83.145 > D8=3D117.340 > D9=3D20.308 > D10=3D180. > D11=3D0.531 > D12=3D-.0388 > D13=3D-179.993 > D14=3D-179.117 > D15=3D-178.898 > D16=3D-165.610 > D17=3D117.345 > D18=3D-121.060 > D19=3D-179.715 > D20=3D124.820 > D21=3D-114.463 > D22=3D-33.512 > D23=3D119.582 > D24=3D-40.216 > D25=3D-177.862 > D26=3D178.644 > > C H O N S 0 > 6-31g* > **** > Cd 0 > lanl2dz > **** > > Cd 0 > lanl2 > > --Link1-- > %chk=3Dhist_CdSH3.chk > %rwf=3D/scratch/hist_CdSH3.rwf > %int=3D/scratch/hist_CdSH3.int > %d2e=3D/scratch/hist_CdSH3.d2e > %nproc=3D2 > %mem=3D2gb > hf/genECP Geom=3DCheck Opt=3D(NoEigen,MaxCycle=3D999) > > hist_Cd3 Optimization w/o ZM > > -2 1 > > C H O N S 0 > 6-31g* > **** > Cd 0 > lanl2dz > **** > > Cd 0 > lanl2 > > --Link1-- > %chk=3Dhist_CdSH3.chk > %rwf=3D/scratch/hist_CdSH3.rwf > %int=3D/scratch/hist_CdSH3.int > %d2e=3D/scratch/hist_CdSH3.d2e > %nproc=3D2 > %mem=3D2gb > hf/genECP Geom=3DCheck Freq > > hist_Cd3 freq > > -2 1 > > C H O N S 0 > 6-31g* > **** > Cd 0 > lanl2dz > **** > > Cd 0 > lanl2 > > The job runs throught the first two opt's but then gives the following > error on the frequency calculation: > Rotational constants (GHZ): 0.4211850 0.2154773 0.1858423 > General basis read from cards: (5D, 7F) > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D > Pseudopotential Parameters > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D > Center Atomic Valence Angular Power = > =20 > Coordinates > Number Number Electrons Momentum of R Exponent = > =20 > Coefficient X Y Z > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= > =3D=3D=3D=3D=3D=3D=3D > EOF while reading ECP pointer card. > Error termination via Lnk1e in /home/local/bin/gaussian/g03/l301.exe at > Sat Nov 12 18:19:20 2005. > Job cpu time: 0 days 0 hours 0 minutes 0.6 seconds. > File lengths (MBytes): RWF=3D 56 Int=3D 0 D2E=3D 0 Chk=3D= > 23 Scr=3D > > I don't understand it as the input for freq ECP is the exact same as the > input for the other opt's that have no problem as far as I can tell. Any > help would be greatly appreciated. Thanks. Cheers, Don Bunk > bunk82(_)newpaltz.edu > > > > --=20 > Computational Chemistry List > Attn. Jan K. Labanowski > Columbus, OH 43221 > http://www.ccl.net > E-mail: chemistry-request(_)ccl.net or ccl(_)ccl.net > > > > --_===28742318====newpaltz.edu===_--> > From owner-chemistry@ccl.net Tue Nov 22 10:30:00 2005 From: "Sean Mooney sdmooney*o*iupui.edu" To: CCL Subject: CCL: CCL and Google Base or Wikipedia Message-Id: <-30035-051122095313-15915-M4AHrSdxgMvcRhYtj2BaMw(-)server.ccl.net> X-Original-From: Sean Mooney Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 22 Nov 2005 09:52:57 -0500 MIME-Version: 1.0 Sent to CCL by: Sean Mooney [sdmooney-$-iupui.edu] I agree wikipedia is powerful. My main point was that if there are some features that wikipedia does not provide that are required by this community, it is possible to install your own version and extend it. -Sean Brian Salter-Duke b_duke**octa4.net.au wrote: > Sent to CCL by: Brian Salter-Duke [b_duke*|*octa4.net.au] > On Mon, Nov 21, 2005 at 09:08:13AM -0500, Sean Mooney sdmooney- > -iupui.edu wrote: > > Sent to CCL by: Sean Mooney [sdmooney]^[iupui.edu] > > Anyone who has worked with academic computational chemistry software > > knows that bugs/errors in docs do occur. The nice thing about wiki's is > > that these errors can be fixed immediately after discovery. In addition > > to protocols, 'factbook' like content is also useful. Wikipedia may not > > be the appropriate place for this, because anyone can change anything > > (including unregistered users) and there is no required structure of the > > documents (like the references mentioned below). However, it is pretty > > easy to install the open source MediaWiki software (the tools that drive > > Wikipedia) if someone were so motivated. This may be attractive > > because required structure can be imposed using templates and limiting > > user access is possible (even if only to registered users, to prevent > > spam). It is also extensible (after overcoming a learning curve), so > > that developers can imbed their own functionality. There are other > > reasons that curent wiki's may not be appropriate for scientific > > knowledgebases. Like the poor controlled vocabulary or ontology > > support, for example. > > I think you underestimate the strength of the open source approach in > Wikipedia. Anyone can alter stuff, but there are users and those > designated as administrators who keep a pretty close eye on changes and > fix "spam" changes quickly. Also "spam" changes are not common, > particularly > in scientific and technical pages. There is a kind of structure and > plenty of peer pressurte to make pages fit the standards. > > A good example of how it works is indeed the Bill Gates page. Have a > look at that page now. It is excellent. > > How do you propose to "impose' structure? Who imposes it? Who decides on > the structure? If there is structure and imposition, people will > probably not do it for free. Who is going to pay them? > > I think the aswer is for us, as a community, to work to improve > wikipedia. Of course not everything suits wikipedia. It is, after all, a > "pedia". Another wiki might be usefull for another purpose, but for > "pedia"-like entries, wikipedia is great and can be better. > > > > If anyone is interested in installing and using a wiki feel free to > > email me offline and I would be happy to chat about some of the issues > > we looked at. > > > > -Sean > > > > Perry E. Metzger perry(!)piermont.com wrote: > > > > >Sent to CCL by: "Perry E. Metzger" [perry/a\piermont.com] > > > > > >"Jim Kress ccl_nospam###kressworks.com" > writes: > > > > > > > > >>Sent to CCL by: "Jim Kress" [ccl_nospam]![kressworks.com] > > >>Except that recent examination has shown Wikipedia to be riddled with > > >>errors, for example: > > >> > > >>http://arstechnica.com/staff/palatine.ars/2005/10/20/1580 > > >> > > >>So, I would be unwilling to rely on it for any serious purpose. > > >> > > >> > > > > > >I routinely correct errors in chemical factboxes on Wikipedia. In > > >general, they aren't too bad. They need more references, the way most > > >of Wikipedia does. I find it is often a good place to go for quick > > >information, errors or no. > > > > > >Perry> > > > > > > -- > Brian Salter-Duke (Brian Duke) b_duke,+,octa4.net.au > Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia > Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ > > Honorary Researcher, Chem., Melbourne Univ. & Med. Chem., Monash Univ.> > > > From owner-chemistry@ccl.net Tue Nov 22 11:05:02 2005 From: "Spencer Ericksen spencer_ericksen{:}hotmail.com" To: CCL Subject: CCL: MC routine for relative orientation of two or more molecules Message-Id: <-30036-051122102446-18358-R5yhVjSN3QD3cGxMFS2cAA|-|server.ccl.net> X-Original-From: "Spencer Ericksen" Content-Type: text/plain; format=flowed Date: Tue, 22 Nov 2005 15:24:34 +0000 Mime-Version: 1.0 Sent to CCL by: "Spencer Ericksen" [spencer_ericksen[a]hotmail.com] If you really want to use MC, Affinity (Accelrys, Inc.) and older versions of AutoDock employ MC techniques that place the molecules together in a large number of different configurations (no program covers all search space). GRAMM-X (server-based docking) or PatchDock may work, but I'm not sure if they use MC methods. In any case, you could use any standard MM docking program first. Then just move the output structures to a QM program for energy calculations. Spencer S. Ericksen, Ph.D. 420 W. Wilson St. Apt. 108 Madison, WI 53703 304-685-7660 ----Original Message Follows---- > From: "Michel Petitjean ptitjean{}itodys.jussieu.fr" Reply-To: "CCL Subscribers" To: "Ericksen, Spencer " Subject: CCL: MC routine for relative orientation of two or more molecules Date: Mon, 21 Nov 2005 06:24:19 -0500 Received: from server.ccl.net ([66.93.212.15]) by mc11-f39.hotmail.com with Microsoft SMTPSVC(6.0.3790.211); Mon, 21 Nov 2005 03:42:26 -0800 Received: from server.ccl.net (ccl [127.0.0.1])by server.ccl.net (8.13.1/8.13.1) with ESMTP id jALBXUWc012836for ; Mon, 21 Nov 2005 06:42:25 -0500 Received: (from root]-[localhost)by server.ccl.net (8.13.1/8.13.1/Submit) id jALBOJe9000956for spencer_ericksen]-[hotmail.com; Mon, 21 Nov 2005 06:24:19 -0500 X-Message-Info: JGTYoYF78jGKs0XkK+pqE2/gHhXv6VNYCiXviOh6yh0= X-Original-From: Michel Petitjean X-Preference-Score: 0 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 Return-Path: owner-chemistry]-[ccl.net X-OriginalArrivalTime: 21 Nov 2005 11:42:26.0457 (UTC) FILETIME=[A5387890:01C5EE90] Sent to CCL by: Michel Petitjean [ptitjean#%#itodys.jussieu.fr] To: Subject: CCL: Re: MC routine for relative orientation of two or more molecules There is an infinity of relative orientations, i.e. rotating and translating one of the molecule, the other having fixed coordinates. May be you could sample: random rotations (isotropic law), and random translations (probability law to be defined carefully). Other problem, how would you like to rank the results, so that you select the best ones? Michel Petitjean, Email: petitjean,+,itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean,+,ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html Sent to CCL by: "Patrik Jens Johansson" [patrikj-#-fy.chalmers.se] >Dear CCLers, > >I would like to investigate two molecules orientation with respect to each other i.e. let one of them rotate and contact the other in all possible ways - distances / angles etc. Preferrably I would like to make lots of HF or higher single point calcs, both molecules treated "stiff", and then choose among these results for further optimisations to final structures. >Any suggestions of a routine or subroutine in an existing software? >(The GLOBOP option in GAMESS does not allow two QM units to be used) > >Sincerely >/Patrik >patrikj(~)fy.chalmers.se >Chalmers Univ. of Technologyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Nov 22 12:14:00 2005 From: "Jim Kress ccl_nospam(a)kressworks.com" To: CCL Subject: CCL: Wikipedia defense Message-Id: <-30037-051122121242-13496-yktIAxP8K/EbrbL+qlxBpw|*|server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 22 Nov 2005 12:12:25 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam]=[kressworks.com] I see a lot of Wikipedia defense going on, even in the face of the demonstrated factual errors incorporated therein ( http://www.wired.com/news/print/0,1294,66210,00.html ). That's fine if you understand that it is the nature of man that something owned by a commune, with everyone responsible for its creation and maintenance, really is owned by no one so has no one is held accountable for its deficiencies. That is why Marxism, Leninism, Maoism, and the rest of the attempts at communist entities (in a true commune sense) have (and will) fail. As for me, I prefer a capitalist approach (like peer reviewed journals and associated databases) where people know who's responsible and can take the action necessary to ensure accountability and success. Regards, Jim Kress "The reformation was preceded by the discovery of America, as if the Almighty graciously meant to open a sanctuary to the persecuted in future years, when home should afford neither friendship nor safety." -- Thomas Paine (Common Sense, 1776) From owner-chemistry@ccl.net Tue Nov 22 13:12:00 2005 From: "Schrodinger Announcements announce..schrodinger.com" To: CCL Subject: CCL: New release of Schrodinger software available Message-Id: <-30038-051122130924-3903-zpCGDIyhCc1AGdt062PHAw^server.ccl.net> X-Original-From: "Schrodinger Announcements" Sent to CCL by: "Schrodinger Announcements" [announce---schrodinger.com] Schrodinger announces the release of two new products: CombiGlide, for rational combinatorial library design; and Epik, for rapid and robust pKa predictions. CombiGlide takes advantage of Glide's XP (extra precision) scoring function to efficiently design focused compound libraries, while Epik combines the proven reliability of Hammett and Taft methods with tautomerization tools to produce reasonable ligand protonation states under biological conditions. To learn more about these new products, please visit the Schrodinger web site at http://www.schrodinger.com. Along with these two new products are new releases of all of Schrodingers software, including Glide, Prime, Phase, MacroModel, Jaguar, Maestro, and more. To find out more about the new releases, please go to http://www.schrodinger.com. From owner-chemistry@ccl.net Tue Nov 22 13:46:00 2005 From: "Bill Ross ross^-^cgl.ucsf.edu" To: CCL Subject: CCL: CCL and Google Base or Wikipedia Message-Id: <-30039-051122131344-8258-oJDNZm1yIwwxLvXxTR0HOA/a\server.ccl.net> X-Original-From: Bill Ross Date: Tue, 22 Nov 2005 09:38:36 -0800 (PST) Sent to CCL by: Bill Ross [ross|a|cgl.ucsf.edu] I would be very hesitant to cite wikipedia because it will change - hopefully for the better - so that in some number of years the citation may not make much sense. Your paper may even become the foundation for the page you cite, wiping out whatever you originally referred to. Wikipedia is a great place to collaboratively organize information, and promises to be a major reference, even if not cited in the sense that fixed media can be cited. Bill Ross From owner-chemistry@ccl.net Tue Nov 22 15:10:01 2005 From: "Michel Petitjean ptitjean[-]itodys.jussieu.fr" To: CCL Subject: CCL: molecular modeling freewares for Mac OS X Message-Id: <-30040-051122150737-16531-1czBJ5ogQFgt1YxB1h67fQ .. server.ccl.net> X-Original-From: Michel Petitjean Date: Tue, 22 Nov 2005 21:07:26 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean,,itodys.jussieu.fr] To: chemistry,ccl.net Subject: CCL: molecular modeling freewares for Mac OS X Dear CCLers, Mac OS X versions of my freewares are now available on my web page: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Please contact me if you encounter problems with them. Thanks. Michel Petitjean, Email: petitjean,itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean,ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From owner-chemistry@ccl.net Tue Nov 22 16:42:00 2005 From: "Brian Salter-Duke b_duke%x%octa4.net.au" To: CCL Subject: CCL: Wikipedia defense Message-Id: <-30041-051122161426-8393-6R59eHo5yTuc1cnzptpaTg!^!server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 23 Nov 2005 08:13:13 +1100 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke*o*octa4.net.au] On Tue, Nov 22, 2005 at 12:15:03PM -0500, Jim Kress ccl_nospam(a)kressworks.com wrote: > Sent to CCL by: "Jim Kress" [ccl_nospam]=[kressworks.com] > I see a lot of Wikipedia defense going on, even in the face of the > demonstrated factual errors incorporated therein ( > http://www.wired.com/news/print/0,1294,66210,00.html ). I note that this article points to errors in areas outside technology, such as ancient history and generally reports that the technology stuff is pretty good. > That's fine if you understand that it is the nature of man that something > owned by a commune, with everyone responsible for its creation and > maintenance, really is owned by no one so has no one is held accountable for > its deficiencies. That is why Marxism, Leninism, Maoism, and the rest of > the attempts at communist entities (in a true commune sense) have (and will) > fail. > > As for me, I prefer a capitalist approach (like peer reviewed journals and > associated databases) where people know who's responsible and can take the > action necessary to ensure accountability and success. I think this introduction of political philosophy here is not helpfull, but since you started it, I'll join in. In mnay capitalist concerns you do not know who is responsible and since those who are responsible are hidden, behind a great mass of money, you can not ensure accountability and success. Back to wikipedia. Bill Ross, in another post, argues about the inability to cite wikipedia. I do not think you should cite it. It is, like all 'pedias', the thing you look at to get a toe into an area. You then move on to more detailed sources. Sean Mooney, in another post, argues for another wiki site if something we need in the CC comunity is not on wikipedea. In many cases it would be better for us to add it. If it really is not 'pedia' material, then sure, another wiki might be needed. For example, there is a new wiki at http://www.compchemwiki.org/index.php?title=Main_Page for computational chemistry data and results. It will be interesting to see how it goes and whether it meets a real need. Does the peer review system give us what we want, particularly in the nature of general reviews intended for the newcomer? Often, it seems to me, they do not. In some cases, just like wikipedea, there are errors. These do not get fixed, as they would in wikipedia. More often the review is biased. It just covers the work of one group or a few related groups and has not real balance. Or it may express tentative opinions as fact. This is where wikipedea is good. For example, in recent days an edit was done on the coupled cluster page. The phrase "It is also one of the most important ab initio methods available in computational quantum chemistry." was taken out and the author of the change commented "I like CC too, but that is over stating things a bit". The wikipedea editors have a good sense of balance and this is sadly lacking in many published reviews. For example, when was the last review on semi-empirical methods written that covered all methods in a critical and fair manner, without favour just to a few methods? To protect the guilty and the inocent, I will not give my answer, but I welcome suggestions for an answer. This does not mean of course that some reviews on semiempirical methods are not valuable. If you just want to learn one or a group of related methods they are. But if you want a critical scholarly account of the whole field many are lacking. BTW, I have yet to check out wikipedia in this area. My main interests so far on wikipedia have been with ab initio methods. I would add here that there are wikipedia administrators who have a good knowledge of the field and who are active in research in computational chemistry. They keep an eye on all articles. I keep a "watch" on all pages I have edited. I then check the changes made by others. Poor pages are usually tagged by someone. The CC page, for example is tagged "This article needs to be cleaned up to conform to a higher standard of quality.". This should warn the user and challenge those who are active in wikipedia editing to do something about it. Maybe I'll meet you there. Cheers, Brian. > Regards, > > Jim Kress > -- Brian Salter-Duke (Brian Duke) b_duke%x%octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher, Chem., Melbourne Univ. & Med. Chem., Monash Univ. From owner-chemistry@ccl.net Tue Nov 22 22:06:00 2005 From: "kalpana krishnaswami kkalpana|,|vsnl.net" To: CCL Subject: CCL: Converting CAS names to structures Message-Id: <-30042-051122211336-5711-HOv3Yg/jXLa7hfxjH5TCJQ[-]server.ccl.net> X-Original-From: "kalpana krishnaswami" Sent to CCL by: "kalpana krishnaswami" [kkalpana _ vsnl.net] Hi: Does anybody know of any 3rd party tools preferably freeware that could convert CAS names to structures? A lot of tools do this with IUPAC names, but I havent been able to find one that converts CAS names. Regards Kalpana From owner-chemistry@ccl.net Tue Nov 22 23:35:00 2005 From: "Ivan Tubert-Brohman ivan.tubert-brohman{}yale.edu" To: CCL Subject: CCL: CCL and Google Base or Wikipedia Message-Id: <-30043-051122225839-31919-UdeME4FFagwTagvkHB4xAw---server.ccl.net> X-Original-From: Ivan Tubert-Brohman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 22 Nov 2005 21:58:34 -0500 MIME-Version: 1.0 Sent to CCL by: Ivan Tubert-Brohman [ivan.tubert-brohman:yale.edu] Bill Ross ross^-^cgl.ucsf.edu wrote: > Sent to CCL by: Bill Ross [ross|a|cgl.ucsf.edu] > I would be very hesitant to cite wikipedia because it will change - > hopefully for the better - so that in some number of years the > citation may not make much sense. That's a non-issue. You can always cite the specific version of the page you are seeing right now, same as any older revision, because all the revisions are archived. This actually makes it more citable than most other websites! Cheers, Ivan