From chemistry-request@ccl.net Wed Apr 28 00:35:28 2004 Received: from mrbusi1.netcologne.de (mrbusi1.netcologne.de [194.8.194.213]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3S5ZQPG006956 for ; Wed, 28 Apr 2004 00:35:27 -0500 Received: from cosmologic.de (xdsl-213-196-244-248.netcologne.de [213.196.244.248]) by mrbusi1.netcologne.de (Postfix) with ESMTP id 5E2A41A0033; Wed, 28 Apr 2004 07:36:47 +0200 (CEST) Message-ID: <408F42ED.6020107=at=cosmologic.de> Date: Wed, 28 Apr 2004 07:36:45 +0200 From: Andreas Klamt User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Liviu Mihail Mirica , chemistry=at=ccl.net Subject: Re: CCL:Frequency job in solvent References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=4.4 required=7.5 tests=MY_BAD_DOT,MY_DSL, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Liviu, I do not know what the reason for your technical problems are. But I definitely know that calculation of the frequencies will not lead you to the free energy in a solvent. In solvents the free energy is domonated by the interactions with the solvent molecules, while the changes in frequencies are of negligible importance. Presently probably the most reliable method for prediction of the free energy of molecules in arbitrary solvents and even mixtures, at variable temperature, is my COSMO-RS method. We are winner of the first industrial fluid property prediction challenge organized by NIST in 2002. In Gaussian03 you have the option to choose the settings to produc e a COSMO file according to our standards. This file can be read by our COMSOtherm program and it gives you the free energy (together with lots of other thermodynamic infiormation). Read more about COSMO-RS on our homepage: www.cosmologic.de. Good luck Andreas Liviu Mihail Mirica wrote: >Hi all, >I have a question regarding a Gaussian98 frequency job in a solvent. The >input section is given below: > >#P gfinput iop(6/7=3) >#P RB3LYP/6-31G* scfcyc=400 >#P guess=read geom=check scrf=(pcm,solvent=thf) freq > >for some reason, the job seems to do the SP calculation in a solvent >over and over again. i let the job to run for a week, and all i got as >about 30 sp jobs. and it keeps going. it never starts calculating the >force constants or so. does anyone know what could be the problem? is the >solvent method i'm uasing the cause for this? is in any way possible to >get the free energy in solvent (that's the reason i'm doing a frequency >job). >Thank you very much. >Sincerely, >Liviu Mirica > > > > >************************** >Liviu Mihail Mirica tel: 650-497-3188 >Escondido Village, 35 B email: liviu=at=leland.stanford.edu >Stanford, CA 94305, USA > > > >-= 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 mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow=at=nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt=at=cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@ccl.net Tue Apr 27 21:18:14 2004 Received: from smtp.goldrush.com (smtp.goldrush.com [206.171.171.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3S2IDPG001357 for ; Tue, 27 Apr 2004 21:18:14 -0500 Received: from [64.162.10.66] (x2-04-66.goldrush.com [64.162.10.66]) by smtp.goldrush.com (8.12.8/8.12.8) with ESMTP id i3S2JYJ4025599; Tue, 27 Apr 2004 19:19:35 -0700 In-Reply-To: <004601c42c66$4f55dcd0$efe27e82@leonidas> References: <004601c42c66$4f55dcd0$efe27e82@leonidas> Mime-Version: 1.0 (Apple Message framework v609) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <431CA606-98BA-11D8-8E89-000393D4953A=at=goldrush.com> Content-Transfer-Encoding: 7bit Cc: chemistry=at=ccl.net From: Stephen Bowlus Subject: Re: CCL:database agrochemicals/insecticides ? Date: Tue, 27 Apr 2004 19:17:56 -0700 To: "Jerome Baudry" X-Mailer: Apple Mail (2.609) X-MailScanner: Found to be clean X-MailScanner-SpamCheck: X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I'm not aware of a database of ag chemicals along the lines of NCI database, but I have not been in that particular field for five or six years (there was _not_ one up until 1999 for sure). Some places to look: Since you are in Champaign, check with researchers at Illinois Natural History Survey. Many moons ago they had very tight connections with extension services and the like, who might know of online resources. Similarly, talk to researchers in the entomology departments and agronomy/ crop sciences departments. In entomology, there used to be an applied effort in vector control. This was run by Robert Metcalf; I'm sure he is retired, but perhaps another researcher is doing this type of work, and they would use similar resources. USEPA will have some of this data, but I don't know if it will be organized in way to be of use to you. I would also look at NIEHS web site. There are some standard reference books, somewhat like the Merck index, but with more extensive monographs, from which a database could be compiled. Google the "Pesticide manual" and/or "Herbicide handbook" Hope this helps, Steve On Apr 27, 2004, at 7:45 AM, Jerome Baudry wrote: > Dear List, > > I am looking for a database of agrochemicals compounds -in particular > insecticides- for use in V-HTS. Preferably in sdf format, but any > electronic > format will do. Any quantity of information is fine, from just the > structure > to catalog #, purity/price etc.. > > Any idea? > > Thanks , > Jerome > > ---------------------------------------------------------- > Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager. > School of Chemical Sciences University of Illinois at > Urbana-Champaign > 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 > Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120; e-mail: > jerome=at=scs.uiuc.edu > > > > -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow=at=nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > > From chemistry-request@ccl.net Tue Apr 27 23:16:52 2004 Received: from rwcrmhc12.comcast.net (rwcrmhc12.comcast.net [216.148.227.85]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3S4GpPG005192 for ; Tue, 27 Apr 2004 23:16:51 -0500 Received: from planaria (c-24-18-175-184.client.comcast.net[24.18.175.184]) by comcast.net (rwcrmhc12) with SMTP id <2004042804181201400i97qje>; Wed, 28 Apr 2004 04:18:12 +0000 Reply-To: From: "Mark Thompson" To: Subject: Validating docking codes. Date: Tue, 27 Apr 2004 21:18:10 -0700 Message-ID: <000201c42cd7$d1078be0$0200a8c0@planaria> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I have a new docking code and scoring function that I'm currently validating. I'm mainly using the data in Wang's J. Med. Chem paper (2003, 46, 2287-2303) and the Gold test set. I've culled most of the docking literature for other "standard" tests. One area where I'm weak is having good ligand libraries for testing database enrichments. I could construct these libraries myself, but then direct comparisons with other docking/scoring methods cited in the literature might be ambiguous. I would appreciate hearing from anyone who knows of any such data sources that are available to the public. Cheers, Mark *************************** Mark Thompson Planaria Software PO Box 55207 Seattle, WA 98155 voice: 206.240.4769 FAX: 206.440.3305 mark-.at.-arguslab.com http://www.arguslab.com *************************** From chemistry-request@ccl.net Wed Apr 28 03:02:06 2004 Received: from collapsed.wormhole.hu (collapsed.wormhole.hu [195.70.35.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3S825PG013393 for ; Wed, 28 Apr 2004 03:02:05 -0500 Received: from ta1.sednet.hu ([212.97.0.169] helo=Moon) by collapsed.wormhole.hu with asmtp (Exim 3.36 #1 (Debian)) id 1BIk2M-0003S4-00; Wed, 28 Apr 2004 10:03:22 +0200 Received: from szilva by Moon with local (Exim 3.36 #1 (Debian)) id 1BIjya-0000kw-00; Wed, 28 Apr 2004 09:59:28 +0200 Date: Wed, 28 Apr 2004 09:59:28 +0200 From: Szilveszter Juhos To: Mark Thompson , chemistry^at^ccl.net Subject: CCL:Validating docking codes. Message-ID: <20040428075928.GC561^at^computer.org> References: <000201c42cd7$d1078be0$0200a8c0@planaria> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <000201c42cd7$d1078be0$0200a8c0@planaria> User-Agent: Mutt/1.5.5.1+cvs20040105i Sender: Szilveszter Juhos X-Spam-Status: No, hits=-0.5 required=7.5 tests=CASHCASHCASH,SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Tue, Apr 27, 2004 at 09:18:10PM -0700, Mark Thompson wrote: > One area where I'm weak is having good ligand libraries for testing database > enrichments. I could construct these libraries myself, but then direct > comparisons with other docking/scoring methods cited in the literature might > be ambiguous. You are right, however, in the recent Glide paper (J. Med. Chem. 2004, 47, 1750-1759 by Halgren et al.) they are using the same ACD set that was used by Bissantz et al. (J. Med. Chem. 2000, 43, 4759-4767) as far as I see. My opinion ACD is really not the best source of lead/drug-like entities. The FlexX people (J. Med. Chem. 2001, 44, 1035-1042) used a subset of WDI. Having WDI (means having $$$) you can make some comparison though it is only the library creation process not the entities you can read from the article. Likely the best thing you can do is to generate your own libs in the same way as it was mentioned in the papers. OTOH, testing with 1000 or so non-native ligands is not necessarily enough: using vHTS usually the top 1% or less of the whole library is purchased and that is the first ten if you are using a 1K lib :/ Cheers: Szilva From chemistry-request@ccl.net Wed Apr 28 09:35:58 2004 Received: from front2.chartermi.net (front2.chartermi.net [24.213.60.124]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3SEZvPG029586 for ; Wed, 28 Apr 2004 09:35:58 -0500 X-Virus-Scanned: by cgpav Received: from [24.236.135.230] (HELO mmserver) by front2.chartermi.net (CommuniGate Pro SMTP 4.0.6) with SMTP id 305560137; Wed, 28 Apr 2004 10:37:20 -0400 Message-ID: <003c01c42d2e$4d1824f0$0901a8c0@mmserver> From: "Jim Kress" To: , "Jesus Rodriguez-Otero" References: <6.0.1.1.1.20031127091300.01c22e80/at/pop.usc.es> Subject: Re: CCL:Pd-ethylene cluster with G98 Date: Wed, 28 Apr 2004 10:37:15 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net > Is this normal? For Gaussian, yes. > Can dft performance be improved? Yes, vastly. Use PC GAMESS. It's 5 to 10 times faster than Gaussian for DFT calculations. Jim ----- Original Message ----- From: "Jesus Rodriguez-Otero" To: Sent: Thursday, November 27, 2003 4:13 AM Subject: CCL:Pd-ethylene cluster with G98 > Hi netters, > > I am comparing the performance of HF, DFT/B3LYP anda MP2 with Gaussian98 in > a simple > calculation of a cluster formed by two Pd atoms and ethylene. To my > surprise, b3lyp is > much slower than HF or MP2; cpu times are > > hf: 3 min. 21 s. > b3lyp: 1 h. 5 min. > mp2: 8 min. 28 s. > > P-IV running LINUX > > this is my input file: > -------------------------------------------------------------------------- ---------- > %chk=pd2etepa.chk > # hf/lanl2mb opt(z-matrix,maxcyc=60) scf(qc,maxcyc=500) > > Title Card Required > > 0 1 > Pd > Pd 1 2.750872 > C 1 B1 2 A1 > C 3 B2 1 A2 2 > D1 > H 4 B3 3 A3 1 > D2 > H 3 B4 4 A4 5 > D3 > H 4 B5 3 A5 6 > D4 > H 3 B6 4 A6 7 > D5 > > B1 2.408742 > B2 1.354929 > B3 1.070182 > B4 1.070143 > B5 1.070035 > B6 1.069670 > A1 76.672064 > A2 107.368541 > A3 120.230124 > A4 119.863439 > A5 119.916731 > A6 120.275618 > D1 1.099106 > D2 90.171155 > D3 0.053786 > D4 -179.938316 > D5 0.015838 > -------------------------------------------------------------------------- ----------------- > > > Is this normal? > Can dft performance be improved? > > > > > \|/ > ( @ @ ) > -------oOo-(_)-oOo------------------------------------------------------ > > Jeszs Rodrmguez-Otero > Departamento de Qummica Fmsica, Facultade de Qummica > Universidade de Santiago > 15782 Santiago de Compostela, (Spain) > Phone: (+34)-981563100 ext 14436, Fax: (+34)-981595012 > qftjesus/at/usc.es > http://web.usc.es/~qftjesus/index.html > > > > > > -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow/at/nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Wed Apr 28 06:35:33 2004 Received: from qcmm9 ([202.103.38.171]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3SBZVPG022195 for ; Wed, 28 Apr 2004 06:35:32 -0500 Received: from 163.com (qcmm9 [10.10.1.9]) by qcmm9 (8.12.8/8.12.8) with ESMTP id i3SBZK9w022148 for ; Wed, 28 Apr 2004 19:35:28 +0800 Message-ID: <408F96F8.2050909^at^163.com> Date: Wed, 28 Apr 2004 19:35:20 +0800 From: scopio User-Agent: Mozilla/5.0 (X11; U; Linux i686; zh-CN; rv:1.2.1) Gecko/20030225 X-Accept-Language: zh-cn,zh MIME-Version: 1.0 To: chemistry^at^ccl.net Subject: How to regain the ouput the information of G03? Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.1 required=7.5 tests=DEAR_SOMETHING, DNS_FROM_RFCI_DSN,NO_RDNS2,WORKSTATION_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear sir, When I optimize a molecule with G03, I delete my input,output and chk file.(*.gjf, *.out, *.chk). However I found it was still running. But I can't get its output information. I have *.d2e,*.int,*.rwf,*.scr. Could you please tell me whether there is a way to get output information? Thanks! ying xiong From chemistry-request@ccl.net Wed Apr 28 02:21:24 2004 Received: from mail.sysarris.soft.net (mail.sysarris.soft.net [164.164.144.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3S7LLPG011835 for ; Wed, 28 Apr 2004 02:21:22 -0500 Received: from ORANGE.sysarris.soft.net (orange.sysarris.soft.net [164.164.144.9]) (authenticated) by mail.sysarris.soft.net (8.11.2/8.11.2) with ESMTP id i3S7HUV22446 for ; Wed, 28 Apr 2004 12:47:30 +0530 Received: from no.name.available by ORANGE.sysarris.soft.net via smtpd (for [164.164.144.6]) with ESMTP; Wed, 28 Apr 2004 12:55:19 +0530 Reply-To: From: "Raju Vishwanathan" To: Subject: Query regarding AutoDock software. Date: Wed, 28 Apr 2004 12:55:33 +0530 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Spam-Status: No, hits=2.1 required=7.5 tests=FVGT_m_MULTI_ODD2, IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Problem with AutoDock 3.0.5. Installed AutoDock in Red Hat Linux 8.0. AutoDock FAQ point no 3 says "I used "get-dockings" to extract the docked conformations. Where is the macromolecule?" http://www.scripps.edu/pub/olson-web/doc/autodock/faq.html#WHERE_MACRO $ get-dockings xk2A.1hvr.dlg { Its working, generates output file xk2A.1hvr.dlg.pdb } $ pdbqtopdb 1hvr.pdbqs >> xk2A.1hvr.dlg.pdb { Not working, shows the following error} awk: /home/raju/src/autodock/dist305/share/pdbtopdb2.awk:49: fatal: Invalid range end: /[0-9][+- ]/ /home/raju/src/autodock/dist305/share/fixatomnames: line 8: 1839 Broken pipe sed -f $AUTODOCK_UTI/fixatomnames.sed $* /home/raju/src/autodock/dist305/share/getpdbrecords: line 2: 1840 Broken pipe egrep "^ATOM|^HETATM|^REMARK|^USER|^END |^TER|^MODEL |^ENDMDL" $* I donot know how to solve this problem. Please let me know how to overcome this problem. Thanking you, Raju Vishwanathan Sr. Consultant - Life Science Division SysArris Software, Bangalore, India From chemistry-request@ccl.net Wed Apr 28 09:35:25 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3SEZNPG029550 for >ccl.net>; Wed, 28 Apr 2004 09:35:23 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 0BDE74839C; Wed, 28 Apr 2004 10:36:02 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 16613-10; Wed, 28 Apr 2004 10:36:02 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com (srvkyem1.americas.sc-world.com [10.16.100.68]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 017D74836F; Wed, 28 Apr 2004 10:36:02 -0400 (EDT) content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 Subject: RE: Frequency job in solvent Date: Wed, 28 Apr 2004 10:36:01 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0047FD44<>srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Frequency job in solvent Thread-Index: AcQswpDW/1ZWQH9jS8ije6WaNtYqIgAaZR1A From: "Shobe, David" >sud-chemieinc.com> To: "Liviu Mihail Mirica" >stanford.edu>, "CCL computational chemistry list (E-mail)" >ccl.net> X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i3SEZPPG029556 Most likely Gaussian is trying to compute the 2nd derivatives by calculating a bunch of single point energies and approximating dE/dx with (delta-E)/(delta-x) etc. Which is all it can do if there are no analytical gradients for your method. It's probably not worth going to all this trouble just for a solvent effect. Question for other CCL-ers: Are solvent effects on vibrational frequencies primarily of electrostatic origin? That is what the SCRF method assumes, isn't it? But I would think that van der Waals forces (otherwise known as bumping into neighboring solvent molecules) would be the main factor. --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request<>ccl.net]On Behalf Of Liviu Mihail Mirica Sent: Tuesday, April 27, 2004 2:35 PM To: chemistry<>ccl.net Subject: CCL:Frequency job in solvent Hi all, I have a question regarding a Gaussian98 frequency job in a solvent. The input section is given below: #P gfinput iop(6/7=3) #P RB3LYP/6-31G* scfcyc=400 #P guess=read geom=check scrf=(pcm,solvent=thf) freq for some reason, the job seems to do the SP calculation in a solvent over and over again. i let the job to run for a week, and all i got as about 30 sp jobs. and it keeps going. it never starts calculating the force constants or so. does anyone know what could be the problem? is the solvent method i'm uasing the cause for this? is in any way possible to get the free energy in solvent (that's the reason i'm doing a frequency job). Thank you very much. Sincerely, Liviu Mirica ************************** Liviu Mihail Mirica tel: 650-497-3188 Escondido Village, 35 B email: liviu<>leland.stanford.edu Stanford, CA 94305, USA -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow<>nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Wed Apr 28 03:00:50 2004 Received: from yangtze.hku.hk (yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3S80nPG013292 for ; Wed, 28 Apr 2004 03:00:50 -0500 Received: from yangtze.hku.hk (yangtze.hku.hk [127.0.0.1]) by yangtze.hku.hk (8.12.8/8.12.8) with ESMTP id i3S7rPuT006745 for ; Wed, 28 Apr 2004 15:53:25 +0800 Received: from localhost (lhhu@localhost) by yangtze.hku.hk (8.12.8/8.12.8/Submit) with ESMTP id i3S7rOmt006741 for ; Wed, 28 Apr 2004 15:53:25 +0800 Date: Wed, 28 Apr 2004 15:53:24 +0800 (HKT) From: HU lihong To: chemistry=at=ccl.net Subject: AUTODOCK Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All, I want to do docking for a protein which contain atom 'P', but autodock have no parameter for this atom. Who can tell me the parameters for 'P' for autodock and how to put these in the parameter files? Many thanks, Holly From chemistry-request@ccl.net Wed Apr 28 11:37:58 2004 Received: from pollux.chem.umn.edu (pollux.chem.umn.edu [128.101.156.56]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3SGbvkh003502 for ; Wed, 28 Apr 2004 11:37:57 -0500 Received: from pollux.chem.umn.edu (localhost [127.0.0.1]) by pollux.chem.umn.edu (8.12.8/8.12.8) with ESMTP id i3SGdGEW024913; Wed, 28 Apr 2004 11:39:21 -0500 (CDT) Received: (from cramer@localhost) by pollux.chem.umn.edu (8.12.8/8.12.8/Submit) id i3SGdA73024911; Wed, 28 Apr 2004 11:39:10 -0500 (CDT) From: Christopher Cramer Message-Id: <200404281639.i3SGdA73024911*at*pollux.chem.umn.edu> Subject: Re: CCL:Frequency job in solvent To: dshobe*at*sud-chemieinc.com (Shobe, David) Date: Wed, 28 Apr 2004 11:39:10 -0500 (CDT) Cc: chemistry*at*ccl.net In-Reply-To: <9DD56492790889439F731F5BD6DACA0047FD44*at*srvkyem1.americas.sc-world.com> from "Shobe, David" at Apr 28, 2004 10:36:01 AM X-Mailer: ELM [version 2.5 PL2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net David, > > Question for other CCL-ers: > Are solvent effects on vibrational frequencies primarily of electrostatic origin? That is what the SCRF method assumes, isn't it? But I would think that van der Waals forces (otherwise known as bumping into neighboring solvent molecules) would be the main factor. > There are several levels of response to your question. Ben-Naim has first codified the intuitively reasonable relationship delta-G(solvation) = delta-G(solute-solvent coupling) + delta-G(delta-Q) where the first term on the right-hand-side is associated with interactions between the solute and the solvent (and changes in interactions between solvent molecules with each other) and the second term is associated with changes in the solute partition function. The most obvious of these would be, for example, if you were considering a change in standard-state volume (e.g., using 1 mol per 24.5 L for your gas-phase standard state and 1 mol per 1 L for your solution standard state). Such a change in standard-state volume leads to a change in the translational partition function that affects the translational entropy and hence affects the free energy of transfer. Of course, there could also be a change in the rotational and vibrational partition functions too! However, this is much trickier than the trivial correction for the standard-state volume. A solute presumably does not HAVE a rotational partition function -- those degrees of freedom are converted into solute/solvent librational modes, the natures of which are quite difficult to determine either experimentally OR theoretically. Hence, essentially all continuum models proceed from the assumption that there is NO delta-Q affect on the electronic, rotational, or vibrational partition functions, and transform experimental data as appropriate to make the standard-state volume a constant, and parameterize against the remaining coupling free energy (thus, by parameterization, any error in the assumption of zero delta-Q gets buried in the fit). Second, as for the coupling free energy itself, it is divided up into electrostatic and non-electrostatic components. The electrostatic part is nearly always determined either from solution of the Poisson or generalized Born equations (using a self-consistent reaction field formalism if the solute is being treated at a QM level) and the non-electrostatic part is typically (but not always) added at the end in a more or less parametric fashion. To the extent that "bumping into other molecules" is associated with a cavitation term that becomes more positive with increasing solvent-accessible surface area along a vibrational mode (as one example of how such a term is often calculated), this affect will appear in a continuum model, as will the electrostatics. However, let us say that you really ARE interested in how solvation affects the vibrational frequencies. It is not necessarily formally correct to recompute the harmonic-oscillator force constants with the dielectric continuum turned on, because the time scale of the vibration may be considerably faster than the bulk dielectric response time of the solvent. That is, vibration is subject to a certain degree of non-equilibrium solvation, but continuum solvent models are equilibrium in nature unless a frequency-dependent dielectric constant is employed. A nice article addressing the precise issue of IR in solution is Rivail, J.-L.; Rinaldi, D.; Dillet, V., "Solvation Effects on Infrared Spectroscopy: A Computational Approach" Mol. Phys. 1996, 89, 1521-1529. A more general discussion of many of the above issues that is, I hope, still very useful, is the review that Don Truhlar and I wrote 5 years ago Cramer, C. J.; Truhlar, D. G., "Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics" Chem. Rev. 1999, 99, 2161-2200. Best regards, Chris -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (612) 597-5275 cramer*at*pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models") From chemistry-request@ccl.net Wed Apr 28 11:03:32 2004 Received: from mtiwmhc13.worldnet.att.net (mtiwmhc13.worldnet.att.net [204.127.131.117]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3SG3VPG002335 for ; Wed, 28 Apr 2004 11:03:31 -0500 Received: from laptop.us.fujitsu.com (206.denver-06rh15rt.co.dial-access.att.net[12.73.181.206]) by worldnet.att.net (mtiwmhc13) with SMTP id <2004042816044511300bv88ce>; Wed, 28 Apr 2004 16:04:46 +0000 Message-Id: <6.0.1.1.2.20040428095243.0355f3e8*at*postoffice.worldnet.att.net> X-Sender: mrmopac*at*postoffice.worldnet.att.net X-Mailer: QUALCOMM Windows Eudora Version 6.0.1.1 Date: Wed, 28 Apr 2004 09:55:48 -0600 To: CHEMISTRY*at*ccl.net From: "James J. P. Stewart" Subject: Re: CCL:Calculation of an angle In-Reply-To: <1082573532.4086c2dc45b7a*at*webmail.u-picardie.fr> References: <1082573532.4086c2dc45b7a*at*webmail.u-picardie.fr> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Given the three distances between each pair of atoms, use the familiar equation: c^2 = a^2 + b^2 - 2abCos(c) or Cos(c) = (a^2 + b^2 - c^2)/(2ab) Given Cos(c) take the inverse to get the angle c. Jimmy At 02:03 PM 4/21/2004, you wrote: >Dear All, > >I am looking for an equation to calculate an angle from the cartesian >coordinates of the 3 atoms making this angle. > ( @ @ ) .-------------oOOo----(_)----oOOo-------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry | E-mail: jstewart*at*us.fujitsu.com | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | | | USA .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo. | | .--------------------\ (----( )-------------------------------------. \_) ) / (_/ From chemistry-request@ccl.net Wed Apr 28 11:50:53 2004 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3SGoqkh003987 for ; Wed, 28 Apr 2004 11:50:52 -0500 Received: from gollum.unb.ca (gollum.unb.ca [131.202.3.51]) by mailserv.unb.ca (8.12.10/8.12.10) with ESMTP id i3SGiQ3v029680; Wed, 28 Apr 2004 13:44:26 -0300 Received: from gollum.unb.ca (localhost.localdomain [127.0.0.1]) by gollum.unb.ca (8.12.8/8.12.8) with ESMTP id i3SGqDAD032124; Wed, 28 Apr 2004 13:52:13 -0300 Received: (from apache@localhost) by gollum.unb.ca (8.12.8/8.12.8/Submit) id i3SGqC1U032118; Wed, 28 Apr 2004 13:52:12 -0300 Received: from raven.chem.unb.ca (raven.chem.unb.ca [131.202.164.46]) by webmail.unb.ca (IMP) with HTTP for ; Wed, 28 Apr 2004 13:52:12 -0300 Message-ID: <1083171132.408fe13c1adc2[at]webmail.unb.ca> Date: Wed, 28 Apr 2004 13:52:12 -0300 From: "Flight, Robert Maxwell" Reply-to: robert.flight[at]unb.ca To: Raju Vishwanathan , Computational Chemistry List Subject: Re: CCL:Query regarding AutoDock software. References: In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.164.46 X-UNB-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: X-MailScanner-From: l72k6[at]unb.ca X-Spam-Status: No, hits=2.6 required=7.5 tests=FROM_HAS_MIXED_NUMS, FVGT_m_MULTI_ODD2,IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Raju, The PDB file from the docking log (get-dockings) command will have the ligands in the same orientation with respect to the macromolecule. You must load the original file (PDB, MOL2, etc) of the macromolecule that you used to create the PDBQS in order to view the interactions of the ligands with the receptor. -Robert *************************** Robert Flight Master Candidate Computational Chemistry Department of Chemistry University of New Brunswick Fredericton NB, Canada E3B 6E2 e-mail: robert.flight[at]unb.ca *************************** "A computer terminal is not some clunky old television with a typewriter in front of it. It is an interface where the mind and body can connect with the universe and move bits of it about." -- Hitch Hikers Guide to the Galaxy Quoting Raju Vishwanathan : > Problem with AutoDock 3.0.5. Installed AutoDock in Red Hat Linux 8.0. > > AutoDock FAQ point no 3 says "I used "get-dockings" to extract the docked > conformations. Where is the macromolecule?" > http://www.scripps.edu/pub/olson-web/doc/autodock/faq.html#WHERE_MACRO > > > $ get-dockings xk2A.1hvr.dlg { Its working, generates output file > xk2A.1hvr.dlg.pdb } > $ pdbqtopdb 1hvr.pdbqs >> xk2A.1hvr.dlg.pdb { Not working, shows the > following error} > > awk: /home/raju/src/autodock/dist305/share/pdbtopdb2.awk:49: fatal: Invalid > range end: /[0-9][+- ]/ > /home/raju/src/autodock/dist305/share/fixatomnames: line 8: 1839 Broken > pipe > sed -f $AUTODOCK_UTI/fixatomnames.sed $* > /home/raju/src/autodock/dist305/share/getpdbrecords: line 2: 1840 Broken > pipe > egrep "^ATOM|^HETATM|^REMARK|^USER|^END |^TER|^MODEL |^ENDMDL" $* > > I donot know how to solve this problem. Please let me know how to overcome > this problem. > > Thanking you, > Raju Vishwanathan > Sr. Consultant - Life Science Division > SysArris Software, Bangalore, India > > > > > > > > -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow[at]nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Wed Apr 28 13:14:42 2004 Received: from nightshade.noc.ucla.edu (nightshade.noc.ucla.edu [169.232.48.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3SIEfkh007127 for ; Wed, 28 Apr 2004 13:14:41 -0500 Received: from azalea.noc.ucla.edu (azalea.noc.ucla.edu [169.232.47.12]) by nightshade.noc.ucla.edu (8.12.11/8.12.11) with ESMTP id i3SIG38Y025058 for ; Wed, 28 Apr 2004 11:16:03 -0700 Received: from ucla.edu (Yang.seas.ucla.edu [128.97.82.197]) (authenticated bits=0) by azalea.noc.ucla.edu (8.12.11/8.12.11) with ESMTP id i3SIFwF0011355 for ; Wed, 28 Apr 2004 11:16:03 -0700 Message-ID: <408FF44F.4070707{at}ucla.edu> Date: Wed, 28 Apr 2004 11:13:35 -0700 From: Douglas Sievers User-Agent: Mozilla Thunderbird 0.5 (X11/20040208) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry{at}ccl.net Subject: Summary: Gaussian 03 32-bit binaries on AMD 64 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Probable-Spam: no X-Spam-Hits: -4.901 X-Scanned-By: vscan.smtp.ucla.edu X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net All, Here is a summary of replies to my original message (bottom). Summarizing an answer, the 32-bit binaries run without a hitch on SuSe linux on AMD64. Also, there is a response from Gaussian stating that they will not test or support Fedora, and they also suggest using SuSe linux. Reply 1 --------------------------- Hi Doug, we have a cluster built with 2 GHz AMD Opteron processors. We have run the 32-bit binaries of Gaussian98 on this system without any problems. Other program's 32-bit binaries have also run without a hitch on this system (as advertised by AMD). We are running SuSE Enterprise and like it alot (system admin is very intuitive). good luck, Kirk Peterson ---------------------------- Reply 2 (from Gaussian support) ---------------------------- Dr. Sievers, We have tested 32 bit binaries and with some versions of Linux they do run. It is a big waste since you won't have access to one of the best features, large disk files and larger memory because of 64 bit addressing. We are finishing the Opteron port and it will be available in our next minor revision. It will be available as an additional platform addendum to your existing license at that time. We have tested with SuSE Linux. Given that Fedora is not going to be a supported OS from RedHat we don't plan on testing or supporting it. I highly recommend you look into SuSE. We are using the Portland Group compilers but if you stick with a binary license that is not an issue. We will have details on what we tested and support at release. ---------------------------- Reply 3 ---------------------------- Dear Doug, I got forwarded your e-mail by a friend. We are running 32bit binaries on 64bit processors. We have not had any major problems with the recent operating system releases SuSe 64 bit linux. We have used binaries supplied on the Gaussian CD (i.e. precompiled binaries) and they work fine. We have used old G98 binaries from a 32bit Red Hat system and they work fine. The only thing that might be a problem is that we have not been able to get a file bigger than 2GB. This is a limitation of the 32 bit binaries. Does this help? Regards Mark Vincent P.S. I should state there was an initial problem with the 64b operating system, but it is fine now. ----------------------------------------------------- > Hi CCLers, > > I am planning to build a workstation with an AMD Athlon 64 Processor (3400+ to be specific). My university > has a site-license for Gaussian 03, but we do not have the source code (at least I do not believe we do). > > I have binaries available for Intel and AMD 32-bit architecture under Linux. Supposedly, the Athlon 64 > processors can run 32 bit and 64 bit applications. I was wondering if anyone has had experience running > 32-bit Gaussian binaries on one of these 64-bit(32-bit compatible) systems. > > I am not so much worried about optimizing performance of Gaussian, as I am in the operability of > GaussView and Gaussian itself. I am planning to run the calculations on a separate cluster, unless they > are small or test calculations that could be handled by a single CPU efficiently. > > Please include what OS you are using in the reply. I would likely choose Fedora Core 1 for AMD64 as > my platform, although I am open to suggestions for alternatives. > > Thank you all! > > Doug Sievers From chemistry-request@ccl.net Wed Apr 28 17:45:43 2004 Received: from pickering.cc.nd.edu (pickering.cc.nd.edu [129.74.250.225]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3SMjgkh015380 for ; Wed, 28 Apr 2004 17:45:42 -0500 Received: from localhost (localhost [127.0.0.1]) by pickering.cc.nd.edu (Switch-3.1.4/Switch-3.1.0) with ESMTP id i3SMl64W005078; Wed, 28 Apr 2004 17:47:06 -0500 (EST) Received: from laptop.ccl.net (laptop.ccl.net [129.74.52.62]) by webmail.nd.edu (IMP) with HTTP for ; Wed, 28 Apr 2004 17:47:06 -0500 Message-ID: <1083192426.4090346a16027.-at-.webmail.nd.edu> Date: Wed, 28 Apr 2004 17:47:06 -0500 From: Jan K Labanowski To: chemistry.-at-.ccl.net Cc: jlabanow.-at-.nd.edu Subject: ChemSketch 5.0 for MS-Windows from ACD/Labs available for free MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 129.74.52.62 X-ND-MTA-Date: Wed, 28 Apr 2004 17:47:07 -0500 (EST) X-ND-Virus-Scan: engine v4.3.20; dat v4354 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net ----- Forwarded message from Scott MacDonald ----- Date: Wed, 28 Apr 2004 17:07:18 -0400 From: Scott MacDonald Reply-To: CHEMICAL INFORMATION SOURCES DISCUSSION LIST Subject: Re: ChemDraw To: CHMINF-L.-at-.LISTSERV.INDIANA.EDU Greetings, Advanced Chemistry Development, Inc., (ACD/Labs) is currently donating campus site licenses of our award winning chemical structure drawing and visualization software, ACD/ChemSketch v5.0 (http://www.acdlabs.com/chemsketch/). ACD/ChemSketch will allow your users to intelligently draw virtually any chemical compound they can imagine, modify it for a specific journal submission, view it in three dimensions, copy and paste it into other Microsoft Windows applications, and obtain an IUPAC name for the compound or other calculated properties, plus a great deal more. If you are curious about this spectacular chemical drawing package, which is already enjoyed by more than 350,000 people, please feel free to download our freeware version from http://www.acdlabs.com/download to evaluate. A partial list of other schools that have accepted our donated site license version of ACD/ChemSketch can be found at http://www.acdlabs.com/educators/chsk_licenses.html Site licenses of our latest version of ChemSketch, ACD/ChemSketch version 7.0 (version 8.0 to be released on the 1st of May) are available for purchase with prices starting at $1,875 US. If you are interested to know how the purchased commercial version differs from our freeware and donated site license software, please contact me. A detailed list of all the features found in the commercial version of ACD/ChemSketch v7.0 can be found at http://www.acdlabs.com/chemsketch/. Please do not hesitate to contact me if you have any questions. Best wishes, Scott MacDonald -- Scott MacDonald Account Manager Advanced Chemistry Development, Inc. (ACD/Labs) 90 Adelaide St. West, Suite 600 Toronto, ON M5H 3V9 Canada Tel: (416) 368-3435 x229 Fax:(416) 368-5596 Toll: 1-800-304-3988 x229 scott.-at-.acdlabs.com www.acdlabs.com I made this drawing in less than five minutes, but it took me sixty years to be able to do that Pierre-Auguste Renoir (1841-1919) Announcing the SC&I 2003 Top Products Award Winners: ACD/ChemSketch and ACD/ChromManager Find out how you can improve ADME properties of your compounds with ACD/MedChem Advisor CONFIDENTIALITY NOTICE: Unless expressly stated otherwise, this message is confidential and is intended for the addressee(s) only. If you are not an addressee, please inform the sender immediately or contact info.-at-.acdlabs.com. ___ ACD/Labs is currently donating site licenses of the commercial version of ACD/ChemSketch v5.0 to any interested academic institution. If you would like additional information on the "ChemSketch site license donation program" please contact me. CHMINF-L Archives (also to join or leave CHMINF-L, etc.) http://listserv.indiana.edu/archives/chminf-l.html Search the CHMINF-L archives at: http://listserv.indiana.edu/cgi-bin/wa?S1=chminf-l Sponsors of CHMINF-L: http://www.indiana.edu/~cheminfo/chminf-l_support.html ----- End forwarded message ----- From chemistry-request@ccl.net Wed Apr 28 16:55:06 2004 Received: from nj.schrodinger.com (tandoori.schrodinger.com [216.216.237.99]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3SLt5kh014270 for ; Wed, 28 Apr 2004 16:55:05 -0500 Received: from neva.schrodinger.com (neva.schrodinger.com [216.216.237.89]) by nj.schrodinger.com (8.12.11/8.12.6) with ESMTP id i3SLu8lj030306; Wed, 28 Apr 2004 17:56:08 -0400 (EDT) (envelope-from halgren[at]schrodinger.com) Date: Wed, 28 Apr 2004 17:56:08 -0400 (EDT) From: Tom Halgren To: Szilveszter Juhos cc: Mark Thompson , , Impact account Subject: Re: CCL:Validating docking codes In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=2.2 required=7.5 tests=CASHCASHCASH,IMPRONONCABLE_1, MY_FNY_WWW,SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, Dr. Juhos - I'd like to point out that we did not use a subset of the ACD in our general database enrichment studies for Glide. It is true that we did base our ligand database on a set of commercially available compounds that we assembed. But as Table 10 in the first Glide paper (J. Med. Chem. 2004, 47, 1739-1750) shows, we selected out a subset of average MW 400 that matched the properties of a subset of the WDI to which we did have access for some 15 properties, including such things as the average numbers of first and higher-row atoms, rotatable bonds, total rings and heteroaromatic rings, charged and neutral hydrogen bond donors and acceptors, and amide hydrogens. The effect of this selection can best be judged by comparing the properties shown in the table for the "puchasable compounds MW 350" and "drug-like compounds MW 360" sets. Your comment actually refers to a very small part of our work -- namely, to the comparisons we made in the second paper (pp. 1750-1759) to the Bissantz work on thymidine kinase and the estrogen receptor. In this work, as stated, we intentionally used the Bissantz/Rognan ACS database preparation, kindly supplied by Dr. Rognan. We agree that this decoy ligand set is not the most representative, and indeed these ligands were not prepared in the manner we would prefer, but we used them so that we could directly compare Glide to FlexX, GOLD and Dock. Thus, these comparisons are "evenhanded". Actually, I might note, these comparision were not in the originally submitted manuscript at all. Rather, they were added to meet the insistence of a referee that comparisons to other methods be included, and this is what we were able to do, with Dr. Rognan's help, on short notice; we don't, after all, have access to the competitive docking codes ourselves. In our own work, we are now preparing to switch our testing protocol to use decoy sets extracted from the WDI, which we now license, and we will be using both 1000-ligand and 10,000-ligand sets. Tom Halgren -------------------------------------------------------------------------- Thomas A. Halgren Chief Technical Officer voice: 646-366-9555 x 106 Schrodinger, Inc. fax: 646-366-9550 120 W 45th Street e-mail: halgren[at]schrodinger.com New York, NY 10036 www.schrodinger.com -------------------------------------------------------------------------- > Hi all, > > As you may have noticed, Szilveszter Juhos wrote to CCL today that we > used the ACD ligand database in our enrichment studies using Glide. This > is incorrect. Should somebody write to him? > > Mee Shelley > > ---------- Forwarded message ---------- > Date: Wed, 28 Apr 2004 09:59:28 +0200 > From: Szilveszter Juhos > To: Mark Thompson , chemistry[at]ccl.net > Subject: CCL:Validating docking codes. > > On Tue, Apr 27, 2004 at 09:18:10PM -0700, Mark Thompson wrote: > > One area where I'm weak is having good ligand libraries for testing database > > enrichments. I could construct these libraries myself, but then direct > > comparisons with other docking/scoring methods cited in the literature might > > be ambiguous. > > You are right, however, in the recent Glide paper (J. Med. Chem. 2004, 47, > 1750-1759 by Halgren et al.) they are using the same ACD set that was > used by Bissantz et al. (J. Med. Chem. 2000, 43, 4759-4767) as far as I > see. My opinion ACD is really not the best source of lead/drug-like > entities. The FlexX people (J. Med. Chem. 2001, 44, 1035-1042) used a > subset of WDI. Having WDI (means having $$$) you can make some > comparison though it is only the library creation process not the > entities you can read from the article. > > Likely the best thing you can do is to generate your own libs > in the same way as it was mentioned in the papers. OTOH, testing with > 1000 or so non-native ligands is not necessarily enough: using vHTS usually > the top 1% or less of the whole library is purchased and that is the > first ten if you are using a 1K lib :/ > > Cheers: > Szilva > > -= 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 mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow[at]nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > _______________________________________________ > Impact-l mailing list > Impact-l[at]www.schrodinger.com > https://www.schrodinger.com/mailman/listinfo/impact-l > From chemistry-request@ccl.net Wed Apr 28 16:12:25 2004 Received: from fidji.vianetworks.es (housing7136.vianetworks.es [213.236.7.136]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i3SLCNkh012801 for ; Wed, 28 Apr 2004 16:12:23 -0500 Received: (qmail 30600 invoked by uid 505); 28 Apr 2004 21:13:42 -0000 Received: from unknown (HELO alumni.unav.es) (81.39.40.195) by correo with SMTP; 28 Apr 2004 21:13:41 -0000 Message-ID: <40901E88.5060709~at~alumni.unav.es> Date: Wed, 28 Apr 2004 23:13:44 +0200 From: Miguel Romero Reply-To: mromero~at~imacyt.org Organization: =?ISO-8859-1?Q?Fundaci=F3n_Hospital_Carlos_Haya?= User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry~at~ccl.net Subject: CCL: FREE SOFTWARE Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.6 required=7.5 tests=SUBJ_ALL_CAPS,SUBJ_FREE_CAP autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, This is the first time I write to the CCL. I am starting a new molecular modeling project in a new research group. I've used comercial modeling software for many time but now I have to switch to something else, preferably a FREE or reasonably priced software. I I am going to work with ligand-protein complexes and I need manipulation software, doking and molecular mechanics (geometry optimization and molecular dynamics) software. It can work under linux or windows sistems. Can anybody help me. thanks in advance for any help! cheers, Miguel ******************************************* Miguel Romero, PhD. Fundacisn Hospital Carlos Haya Avda. Carlos Haya 82, Pabellsn A, 7*planta 29010 Malaga Spain Phone: +34 952307928 Fax: +34 951030447 web: http://www.fhch.net e-mail: mromero~at~imacyt.org *******************************************