From owner-chemistry@ccl.net Fri Feb 3 05:07:02 2006 From: "Demetrios Xenides Demetrios.Xenides^uibk.ac.at" To: CCL Subject: CCL:G: LANL2DZ calculation Message-Id: <-30766-060203050052-30549-4tjI+jegi7Mpd9mm7q3Taw**server.ccl.net> X-Original-From: Demetrios Xenides Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 03 Feb 2006 11:04:17 +0100 MIME-Version: 1.0 Sent to CCL by: Demetrios Xenides [Demetrios.Xenides,+,uibk.ac.at] zjwu zjwu..imr.edu wrote: >Sent to CCL by: "zjwu" [zjwu- -imr.edu] >Dear O'Boyle, > >Thank you very much for your information. I have checked the website you provided, and found that for transition metals, the d and p polarization functions are still needed to be input manually, similar to f polarizations. Here in the following, I list my input files, and hope you or someone else can give me more suggeastions. > >Input file: > >------------------- > >#p b3lyp/gen gfinput pseudo=read opt scf(maxcycle=1024) > >Title Card Required > >0 5 >C >W 1 R > >R 2.0 > >C 0 >6-311++g(df) >**** >W 0 >S 3 1.00 > .2137000000D+01 -.1391615001D+01 > .1347000000D+01 .1751026001D+01 > .4366000000D+00 .4694647003D+00 >S 4 1.00 > .2137000000D+01 .1298509209D+01 > .1347000000D+01 -.1810243292D+01 > .4366000000D+00 -.1084453175D+01 > .1883000000D+00 .1258062203D+01 >S 1 1.00 > .5180000000D-01 .1000000000D+01 >P 3 1.00 > .3005000000D+01 -.2405563124D+00 > .1228000000D+01 .7364092379D+00 > .4415000000D+00 .4881487251D+00 >P 2 1.00 > .4010000000D+00 -.1497499457D+00 > .9000000000D-01 .1070746327D+01 >P 1 1.00 > .2800000000D-01 .1000000000D+01 >D 2 1.00 > .9519000000D+00 .4985264991D+00 > .3270000000D+00 .6111109988D+00 >D 1 1.00 > .1054000000D+00 .1000000000D+01 >F 1 1.00 > .8230000000D+00 .1000000000D+01 >**** > >W 0 >S 3 1.00 > .2137000000D+01 -.1391615001D+01 > .1347000000D+01 .1751026001D+01 > .4366000000D+00 .4694647003D+00 >S 4 1.00 > .2137000000D+01 .1298509209D+01 > .1347000000D+01 -.1810243292D+01 > .4366000000D+00 -.1084453175D+01 > .1883000000D+00 .1258062203D+01 >S 1 1.00 > .5180000000D-01 .1000000000D+01 >P 3 1.00 > .3005000000D+01 -.2405563124D+00 > .1228000000D+01 .7364092379D+00 > .4415000000D+00 .4881487251D+00 >P 2 1.00 > .4010000000D+00 -.1497499457D+00 > .9000000000D-01 .1070746327D+01 >P 1 1.00 > .2800000000D-01 .1000000000D+01 >D 2 1.00 > .9519000000D+00 .4985264991D+00 > .3270000000D+00 .6111109988D+00 >D 1 1.00 > .1054000000D+00 .1000000000D+01 >F 1 1.00 > .8230000000D+00 .1000000000D+01 >**** > > > >Please note that the basis set for W is the standard basis set LANL2DZ in Gaussian except F component. F Component is added manually. For standard basis set without F components, it looks like: > > > >#p b3lyp/gen gfinput pseudo=read opt scf(maxcycle=1024) > >Title Card Required > >0 5 >C >W 1 R > >R 2.0 > >C 0 >6-311++g(df) >**** >W 0 >LANL2DZ >**** > >W 0 >LANL2DZ > >this job works perfectly. > >But I run the job with F component included, I met the following error message: > >------------ > > WANTED AN INTEGER AS INPUT. > FOUND A FLOATING POINT NUMBER AS INPUT. > S 3 1.00 > > Error termination via Lnk1e in /opt/g03/g03/l301.exe at Thu Feb 2 17:53:53 200 >6. > Job cpu time: 0 days 0 hours 0 minutes 2.1 seconds. > >------------ > >I think this is related to the format of the basis set, but do not know how to remedy it. > >I appreaciate very much if you have any suggestions. > >Thank you. > >Z. J. Wu > >-------------------------------------------------------------------------------- > > > >>From: Noel O'Boyle >> >> >To: zhijw.\a/.hotmail.com >Subject: Re: CCL: LANL2DZ calculation >Date: Thu, 02 Feb 2006 08:59:13 +0000 > > >>Have you seen "LanL2DZdp ECP" at >>http://www.emsl.pnl.gov/forms/basisform.html? Does this help to give you >>ideas?> > > > Dear Wu You just have to add the "extrabasis" keyword in your route card Cheers Demetrios From owner-chemistry@ccl.net Fri Feb 3 05:42:05 2006 From: "George V Papamokos me00109]_[cc.uoi.gr" To: CCL Subject: CCL:G: working with charges Message-Id: <-30767-060203051212-884-c6ALrj/CA4OxMQHqHT4q1A]*[server.ccl.net> X-Original-From: "George V Papamokos" Sent to CCL by: "George V Papamokos" [me00109###cc.uoi.gr] Dear cclers, Iam currently working with charged oligopeptides. These peptides are multiply charged (positive and negative charges) resulting to a total charge either positive or negative. in the input of gaussian software i can give the total charge of the molecule but how do I know that this is distributed as it should be? For example, an oxygen is connected with a single bond with a carbon atom and it carries a -1 charge. Two nitrogens are also connencted with two other Carbon atoms and they carry a +1 charge each. Total charge -1. I declare the total charge in the first lines of the input (1 1 ) but how do I know that the charges are correctly distributed to the proper atoms? Is it just a matter of bond distances? Thank you in advance. George Papamokos From owner-chemistry@ccl.net Fri Feb 3 08:57:01 2006 From: "Anastasios Papadopoulos anastp.:.chem.auth.gr" To: CCL Subject: CCL: Polarization functions Ag atom Message-Id: <-30768-060203052702-7069-wVyHGiFQEfUrpTWJ8TpocA[A]server.ccl.net> X-Original-From: Anastasios Papadopoulos Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-7; format="flowed" Date: Fri, 03 Feb 2006 12:26:53 +0200 MIME-Version: 1.0 Sent to CCL by: Anastasios Papadopoulos [anastp : chem.auth.gr] Hi CCL subsscribers. I run Ag,Cu clusters using BP86 method and LANL2DZ basis set, in Gausssian 03W B-02 package.In addition, I added extrabasis in Cu atom (6-31G(3d)).Moreover, I want to add an extra f polarization function in Ag atom.Could someone inform me,which coefficients and exponennts exist for f function or where I can find polarization functions for Ag atom? Yours, Tasos G. Papadopoulos Laboratory of Applied Quantum Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki,Greece. From owner-chemistry@ccl.net Fri Feb 3 09:32:01 2006 From: "Anastasios Papadopoulos anastp _ chem.auth.gr" To: CCL Subject: CCL: LANL2DZ calculation Message-Id: <-30769-060203054522-13573-oKVz50rHkQRry6MDf1ml2g|server.ccl.net> X-Original-From: Anastasios Papadopoulos Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-7; format="flowed" Date: Fri, 03 Feb 2006 12:45:11 +0200 MIME-Version: 1.0 Sent to CCL by: Anastasios Papadopoulos [anastp===chem.auth.gr] You can add a keyword "extrabasis" in route. Tasos G. Papadopoulos Laboratory of Applied Quantum Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, Greece From owner-chemistry@ccl.net Fri Feb 3 10:07:01 2006 From: "Thomas Steinbrecher steinbrt^-^uni-freiburg.de" To: CCL Subject: CCL: Ligand Docking with GOLD Message-Id: <-30770-060203075420-10721-DtAmMLLO0lDDc3/R3Evatg/a\server.ccl.net> X-Original-From: "Thomas Steinbrecher" Sent to CCL by: "Thomas Steinbrecher" [steinbrt[a]uni-freiburg.de] Dear CCLers, can somebody point me to a review article that compares the performance of the GOLD ligand docking program to other commonly available docking tools like FlexX, AutoDock etc. ? Kind Regards, Thomas Steinbrecher From owner-chemistry@ccl.net Fri Feb 3 10:42:01 2006 From: "Nuno A.G. Bandeira nuno.bandeira!A!ist.utl.pt" To: CCL Subject: CCL: Polarization functions Ag atom Message-Id: <-30771-060203100140-9813-frxas/4RFX6MuFTYTaVqVA[*]server.ccl.net> X-Original-From: "Nuno A.G. Bandeira" Sent to CCL by: "Nuno A.G. Bandeira" [nuno.bandeira-*-ist.utl.pt] Anastasios Papadopoulos anastp.:.chem.auth.gr wrote: > Sent to CCL by: Anastasios Papadopoulos [anastp : chem.auth.gr] > Hi CCL subsscribers. > > I run Ag,Cu clusters using BP86 method and LANL2DZ basis set, in Gausssian 03W > B-02 package.In addition, I added extrabasis in Cu atom (6-31G(3d)).Moreover, I > want to add an extra f polarization function in Ag atom.Could someone inform > me,which coefficients and exponennts exist for f function or where I can find > polarization functions for Ag atom? f exp.= 1.611 coef. =1 Ehlers et al Chem. Phys. Lett. 1993,208(1,2),111 -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student () IST,Lisbon -- From owner-chemistry@ccl.net Fri Feb 3 11:16:00 2006 From: "Sebastian H. Riedel sebastian.riedel/./mail.uni-wuerzburg.de" To: CCL Subject: CCL: AW: Polarization functions Ag atom Message-Id: <-30772-060203104111-6033-LaJ3Ien0VqEj/dqtbKbz8g\a/server.ccl.net> X-Original-From: "Sebastian H. Riedel" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 3 Feb 2006 15:38:43 +0100 MIME-Version: 1.0 Sent to CCL by: "Sebastian H. Riedel" [sebastian.riedel]|[mail.uni-wuerzburg.de] You can find for every transition metal a polarization function in the paper of A. W. Ehlers, M. Bohme, S. Dapprich, A. Gobbi, A. Hollwarth, V. Jonas, K. F. Kohler, R. Stegmann, A. Veldkamp, G. Frenking, Chem. Phys. Lett. 1993, 208, 111. For Ag it is 1.611 Regards S. Riedel -------------------------------------------- Dipl. Chem. Sebastian H. Riedel Workgroup Prof. Dr. M. Kaupp Institut für Anorganische Chemie University Würzburg Am Hubland D-97074 Würzburg, Germany Phone: +49-931-888-5495 E-mail: sebastian.riedel-x-mail.uni-wuerzburg.de www: http://www-anorganik.chemie.uni-wuerzburg.de/kaupp www: http://www.psichem.de -------------------------------------------- -----Ursprüngliche Nachricht----- Von: owner-chemistry-x-ccl.net [mailto:owner-chemistry-x-ccl.net] Gesendet: Freitag, 3. Februar 2006 15:12 An: Riedel, S Betreff: CCL: Polarization functions Ag atom Sent to CCL by: Anastasios Papadopoulos [anastp : chem.auth.gr] Hi CCL subsscribers. I run Ag,Cu clusters using BP86 method and LANL2DZ basis set, in Gausssian 03W B-02 package.In addition, I added extrabasis in Cu atom (6-31G(3d)).Moreover, I want to add an extra f polarization function in Ag atom.Could someone inform me,which coefficients and exponennts exist for f function or where I can find polarization functions for Ag atom? Yours, Tasos G. Papadopoulos Laboratory of Applied Quantum Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki,Greece.http://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 Fri Feb 3 11:52:01 2006 From: "Paul Hawkins phawkins[]eyesopen.com" To: CCL Subject: CCL: Ligand Docking with GOLD Message-Id: <-30773-060203110310-24547-JTPapeizhujmyRnoDBfJvA/./server.ccl.net> X-Original-From: Paul Hawkins Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 03 Feb 2006 09:00:32 -0700 MIME-Version: 1.0 Sent to CCL by: Paul Hawkins [phawkins:+:eyesopen.com] Try these for a starting point: Warren et al J. Med. Chem., 2005 ASAP. Cummings et al J. Med. Chem., 2005, 48, 962. Bissantz et al J. Med. Chem., 200, 43, 4759. Chen et al. JCIM 2006, 46, 401. Kontoyanni et al. J. Comput. Chem., 2005, 26, 11. Evers et al. J. Med. Chem., 2005, 48, 962 and 1088. Kellenberger et al. Proteins, 2004, 57, 225. Cotesta et al. Proteins, 2005, 60, 629. Klon et al. JCICS, 2004, 44, 2216. Thomas et al., J. Med. Chem., 2006, 49, 92. Vigers and Rizzi, J. Med. Chem., 2004, 47, 80. Docking comparisons have been very popular lately......... But see Cole et al. Proteins, 2005, 60, 325 for some caveats on these sorts of comparisons. Paul. Paul Hawkins Senior Applications Scientist OpenEye Scientific Software Thomas Steinbrecher steinbrt^-^uni-freiburg.de wrote: >Sent to CCL by: "Thomas Steinbrecher" [steinbrt[a]uni-freiburg.de] >Dear CCLers, > >can somebody point me to a review article that compares the performance of the GOLD ligand docking program to other commonly available docking tools like FlexX, AutoDock etc. ? > >Kind Regards, > >Thomas Steinbrecher> > > > From owner-chemistry@ccl.net Fri Feb 3 12:30:01 2006 From: "Ivanciuc, Ovidiu I. oiivanci^^^utmb.edu" To: CCL Subject: CCL: Ligand Docking with GOLD Message-Id: <-30774-060203122727-702-vHw37uiVNlpHiuGnaViDIA|,|server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Fri, 3 Feb 2006 10:25:06 -0600 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci---utmb.edu] >>can somebody point me to a review article that compares >> the performance of the GOLD ligand docking program to >> other commonly available docking tools like FlexX, AutoDock etc. ? Just make a search with the above key-words (i.e., "gold AND flexx" or "gold AND autodock") in PubMed, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed and read the abstracts. Best regards, Ovidiu ********************************* Dr. Ovidiu Ivanciuc Sealy Center for Structural Biology, Department of Human Biological Chemistry & Genetics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1157 USA From owner-chemistry@ccl.net Fri Feb 3 13:04:00 2006 From: "JAMES VIVIAN jamestvivian,+,msn.com" To: CCL Subject: CCL: Ligand Docking with GOLD Message-Id: <-30775-060203113512-9783-zZlk6rggq8dixYUQZRMiQg**server.ccl.net> X-Original-From: "JAMES VIVIAN" Content-Type: text/plain; format=flowed Date: Fri, 03 Feb 2006 11:35:00 -0500 Mime-Version: 1.0 Sent to CCL by: "JAMES VIVIAN" [jamestvivian..msn.com] Thomas: Enjoy! Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shaw, D. E.; Shelley, M.; Perry, J. K.; Francis, P.; Shenkin, P. S, "Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy", J. Med. Chem. 2004, 47, 1739-1749. Kellenberger, E.; Rodrigo, J.; Muller, P.; Rognan, D., "Comparative evaluation of eight docking tools for docking and virtual screening accuracy", Proteins. 2004, 57, 225-242. Perola, E.; Walters, W.P.; Charifson, P.S., "A Detailed Comparison of Current Docking and Scoring Methods on Systems of Pharmaceutical Relevance", Proteins, 2004, 56, 235-249. Kontoyianni, M.; McClellan, L. M.; Sokol, G. S., "Evaluation of Docking Performance: Comparative Data on Docking Algorithms", J. Med. Chem. 2004, 47, 558-565. >From: "Thomas Steinbrecher steinbrt^-^uni-freiburg.de" > >Reply-To: "CCL Subscribers" >To: "Vivian, James T " >Subject: CCL: Ligand Docking with GOLD >Date: Fri, 3 Feb 2006 10:08:06 -0500 > >Sent to CCL by: "Thomas Steinbrecher" [steinbrt[a]uni-freiburg.de] >Dear CCLers, > >can somebody point me to a review article that compares the performance of >the GOLD ligand docking program to other commonly available docking tools >like FlexX, AutoDock etc. ? > >Kind Regards, > >Thomas Steinbrecher> > > From owner-chemistry@ccl.net Fri Feb 3 14:06:00 2006 From: "Lin Teng linteng118-*-hotmail.com" To: CCL Subject: CCL: Ligand Docking with GOLD Message-Id: <-30776-060203124621-23237-8BGWz6bLCrYazSdRpU+21A__server.ccl.net> X-Original-From: "Lin Teng" Content-Type: text/plain; format=flowed Date: Fri, 03 Feb 2006 11:59:09 -0500 Mime-Version: 1.0 Sent to CCL by: "Lin Teng" [linteng118,,hotmail.com] "Evaluation of Docking Performance: Comparative Data on Docking Algorithms," J. Med. Chem., Kontoyianni, M.; McClellan, L. M.; Sokol, G. S., 2004; 47(3); 558-565. Teng >From: "Thomas Steinbrecher steinbrt^-^uni-freiburg.de" > >Reply-To: "CCL Subscribers" >To: "Lin, Teng " >Subject: CCL: Ligand Docking with GOLD >Date: Fri, 3 Feb 2006 10:07:46 -0500 >Received: from server.ccl.net ([66.93.212.15]) by >bay0-mc1-f4.bay0.hotmail.com with Microsoft SMTPSVC(6.0.3790.211); Fri, 3 >Feb 2006 07:40:08 -0800 >Received: from server.ccl.net (ccl [127.0.0.1])by server.ccl.net >(8.13.1/8.13.1) with ESMTP id k13FaaKH026174for ; >Fri, 3 Feb 2006 10:40:05 -0500 >Received: (from root*o*localhost)by server.ccl.net (8.13.1/8.13.1/Submit) id >k13F7kD1017597for linteng118*o*hotmail.com; Fri, 3 Feb 2006 10:07:46 -0500 >X-Message-Info: JGTYoYF78jEgIbE1b3ELxh2VVQ2KUEWyErkPlzDVYnw= >X-Original-From: "Thomas Steinbrecher" >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*o*ccl.net >X-OriginalArrivalTime: 03 Feb 2006 15:40:10.0785 (UTC) >FILETIME=[1DFDB110:01C628D8] > >Sent to CCL by: "Thomas Steinbrecher" [steinbrt[a]uni-freiburg.de] >Dear CCLers, > >can somebody point me to a review article that compares the performance of >the GOLD ligand docking program to other commonly available docking tools >like FlexX, AutoDock etc. ? > >Kind Regards, > >Thomas Steinbrecher> > > From owner-chemistry@ccl.net Fri Feb 3 14:41:01 2006 From: "Jonathan Essex J.W.Essex!^!soton.ac.uk" To: CCL Subject: CCL: second meeting announcement Message-Id: <-30777-060203140239-29112-QipJIhavG8rYVJbanAZX0w[a]server.ccl.net> X-Original-From: Jonathan Essex Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 03 Feb 2006 18:16:45 +0000 MIME-Version: 1.0 Sent to CCL by: Jonathan Essex [J.W.Essex . soton.ac.uk] ++++++++++++++++++++++++++++ 2nd ANNOUNCEMENT DOCKING AND SCORING IN STRUCTURE GUIDED DRUG DESIGN: Call for Papers, Registration Open. NOTE: New deadline for abstracts April 5th - 7th 2006 Molecular Graphics and Modelling Society University of Southampton, United Kingdom Registration is now open for this meeting looking at docking, scoring and free energy calculations in Structure Guided Drug Design. The conference brings together experts in the field of docking and scoring, with a particular emphasis on solvation and free energy methods. Case studies are also included so as to highlight the crucial role of these methods in drug discovery today. Plenary speakers: Ruben Abagyan, Scripps Research Institute; Chris Chipot, Universite Henri Poincare; Andrew Good, Bristol-Myers Squibb; William Jorgensen, Yale University; Andrew Leach, GlaxoSmithKline; Hans Matter, Sanofi-Aventis; Didier Rognan, Universite Louis Pasteur; Marcel Verdonk, Astex Therapeutics Abstracts for contributed oral presentations and for posters are invited, and the closing date is 17th February. Abstracts received after this date will be considered if there is available space in the schedule, but will miss the main prioritisation. There are a limited number of student bursaries, kindly sponsored by CCG. Please see the conference website for more information www.soton.ac.uk/~jwe1/main.html or contact Dr Christine Richardson (c.richardson-#-vernalis.com) or Dr Jonathan Essex (jwe1-#-soton.ac.uk). Closing date for registration is 5th March, 2006 -- Dr Jonathan W. Essex Phone: +44 (0)23 8059 2794 School of Chemistry Fax: +44 (0)23 8059 3781 University of Southampton Email: j.w.essex-#-soton.ac.uk Highfield http://www.soton.ac.uk/~chemphys/jessex Southampton SO17 1BJ United Kingdom From owner-chemistry@ccl.net Fri Feb 3 15:16:00 2006 From: "Mireille Krier mv.krier _ googlemail.com" To: CCL Subject: CCL: Ligand Docking with GOLD Message-Id: <-30778-060203134145-24667-eu1NsLLR5OVtozQ9HU8dmg[#]server.ccl.net> X-Original-From: Mireille Krier Content-Type: multipart/alternative; boundary="----=_Part_9411_11785380.1138988666000" Date: Fri, 3 Feb 2006 18:44:26 +0100 MIME-Version: 1.0 Sent to CCL by: Mireille Krier [mv.krier() googlemail.com] ------=_Part_9411_11785380.1138988666000 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Thomas, may I suggest you the following articles Kellenberger E, Rodrigo J, Muller P, Rognan D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins. 2004 Nov 1;57(2):225-42. Kontoyianni M, McClellan LM, Sokol GS. Evaluation of docking performance: comparative data on docking algorithms. J Med Chem. 2004 Jan 29;47(3):558-65. With best regards, Mireille Krier On 2/3/06, Thomas Steinbrecher steinbrt^-^uni-freiburg.de < owner-chemistry:-:ccl.net> wrote: > > Sent to CCL by: "Thomas Steinbrecher" [steinbrt[a]uni-freiburg.de] > Dear CCLers, > > can somebody point me to a review article that compares the performance o= f > the GOLD ligand docking program to other commonly available docking tools > like FlexX, AutoDock etc. ? > > Kind Regards, > > Thomas Steinbrecher > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > ------=_Part_9411_11785380.1138988666000 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Dear Thomas,
 
may I suggest you the following articles
 
Kellenberger E, Rodrigo J, Muller P, Rognan D.
Comparative evaluat= ion of eight docking tools for docking and virtual screening accuracy.
P= roteins. 2004 Nov 1;57(2):225-42.
 
Kontoyianni M, McClellan LM, Sokol GS.
Evaluation of docking perfo= rmance: comparative data on docking algorithms.
J Med Chem. 2004 Jan 29;= 47(3):558-65.
 
With best regards,
 
Mireille Krier

 
On 2/3/06, T= homas Steinbrecher steinbrt^-^uni-freiburg.d= e <owner-chemistry:-:cc= l.net > wrote:
Sent to CCL by: "Thomas&nbs= p; Steinbrecher" [steinbrt[a]uni-f= reiburg.de ]
Dear CCLers,

can somebody point me to a review article that com= pares the performance of the GOLD ligand docking program to other commonly = available docking tools like FlexX, AutoDock etc. ?

Kind Regards,

Thomas Steinbrecher



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------=_Part_9411_11785380.1138988666000-- From owner-chemistry@ccl.net Fri Feb 3 15:51:00 2006 From: "Shobe, David dshobe * sud-chemieinc.com" To: CCL Subject: CCL:G: LANL2DZ calculation Message-Id: <-30779-060203144811-22308-D+F/C9NcgbCixHzLA7aphg]=[server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 3 Feb 2006 20:47:56 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe|a|sud-chemieinc.com] Since you're NOT changing the pseudopotential, but using the standard LANL2DZ pseudopotential, you can just put LANL2DZ for the pseudo=read input. This will avoid any formatting errors. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry : ccl.net [mailto:owner-chemistry : ccl.net] Sent: Thursday, February 02, 2006 11:30 PM To: Shobe, David Subject: CCL:G: LANL2DZ calculation Sent to CCL by: "zjwu" [zjwu- -imr.edu] Dear O'Boyle, Thank you very much for your information. I have checked the website you provided, and found that for transition metals, the d and p polarization functions are still needed to be input manually, similar to f polarizations. Here in the following, I list my input files, and hope you or someone else can give me more suggeastions. Input file: ------------------- #p b3lyp/gen gfinput pseudo=read opt scf(maxcycle=1024) Title Card Required 0 5 C W 1 R R 2.0 C 0 6-311++g(df) **** W 0 S 3 1.00 .2137000000D+01 -.1391615001D+01 .1347000000D+01 .1751026001D+01 .4366000000D+00 .4694647003D+00 S 4 1.00 .2137000000D+01 .1298509209D+01 .1347000000D+01 -.1810243292D+01 .4366000000D+00 -.1084453175D+01 .1883000000D+00 .1258062203D+01 S 1 1.00 .5180000000D-01 .1000000000D+01 P 3 1.00 .3005000000D+01 -.2405563124D+00 .1228000000D+01 .7364092379D+00 .4415000000D+00 .4881487251D+00 P 2 1.00 .4010000000D+00 -.1497499457D+00 .9000000000D-01 .1070746327D+01 P 1 1.00 .2800000000D-01 .1000000000D+01 D 2 1.00 .9519000000D+00 .4985264991D+00 .3270000000D+00 .6111109988D+00 D 1 1.00 .1054000000D+00 .1000000000D+01 F 1 1.00 .8230000000D+00 .1000000000D+01 **** W 0 S 3 1.00 .2137000000D+01 -.1391615001D+01 .1347000000D+01 .1751026001D+01 .4366000000D+00 .4694647003D+00 S 4 1.00 .2137000000D+01 .1298509209D+01 .1347000000D+01 -.1810243292D+01 .4366000000D+00 -.1084453175D+01 .1883000000D+00 .1258062203D+01 S 1 1.00 .5180000000D-01 .1000000000D+01 P 3 1.00 .3005000000D+01 -.2405563124D+00 .1228000000D+01 .7364092379D+00 .4415000000D+00 .4881487251D+00 P 2 1.00 .4010000000D+00 -.1497499457D+00 .9000000000D-01 .1070746327D+01 P 1 1.00 .2800000000D-01 .1000000000D+01 D 2 1.00 .9519000000D+00 .4985264991D+00 .3270000000D+00 .6111109988D+00 D 1 1.00 .1054000000D+00 .1000000000D+01 F 1 1.00 .8230000000D+00 .1000000000D+01 **** Please note that the basis set for W is the standard basis set LANL2DZ in Gaussian except F component. F Component is added manually. For standard basis set without F components, it looks like: #p b3lyp/gen gfinput pseudo=read opt scf(maxcycle=1024) Title Card Required 0 5 C W 1 R R 2.0 C 0 6-311++g(df) **** W 0 LANL2DZ **** W 0 LANL2DZ this job works perfectly. But I run the job with F component included, I met the following error message: ------------ WANTED AN INTEGER AS INPUT. FOUND A FLOATING POINT NUMBER AS INPUT. S 3 1.00 Error termination via Lnk1e in /opt/g03/g03/l301.exe at Thu Feb 2 17:53:53 200 6. Job cpu time: 0 days 0 hours 0 minutes 2.1 seconds. ------------ I think this is related to the format of the basis set, but do not know how to remedy it. I appreaciate very much if you have any suggestions. Thank you. Z. J. Wu -------------------------------------------------------------------------------- > From: Noel O'Boyle To: zhijw. : .hotmail.com Subject: Re: CCL: LANL2DZ calculation Date: Thu, 02 Feb 2006 08:59:13 +0000 >Have you seen "LanL2DZdp ECP" at >http://www.emsl.pnl.gov/forms/basisform.html? Does this help to give >you ideas?http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Fri Feb 3 16:25:00 2006 From: "William Griffin wogriffin#,#ualr.edu" To: CCL Subject: CCL:G: g03 ab initio heavy atoms Message-Id: <-30780-060203151406-3812-jJeaYDk1EF2KHbBnoRYBSw**server.ccl.net> X-Original-From: "William Griffin" Sent to CCL by: "William Griffin" [wogriffin-*-ualr.edu] Hi, I've been tinkering with this for a while in my grad studies, and I was hoping the CCL community could help. I'm trying to model some small clusters (1-3 atoms) of heavy atoms (Mg through about U) with an ab initio method (B3PW91) and I'm figuring my basis set is what's leading me astray. Any suggestions on ab initio methods/ heavy atom basis sets with gaussian 03? I'm not in love with B3PW91, either. Thanks. William Griffin From owner-chemistry@ccl.net Fri Feb 3 18:34:01 2006 From: "zjwu zjwu^imr.edu" To: CCL Subject: CCL: LANL2DZ calculation Message-Id: <-30781-060203183153-9170-tvgWYgaXviiiv2ZuBR7q7g:server.ccl.net> X-Original-From: "zjwu" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Sat, 4 Feb 2006 08:35:48 +0900 Mime-Version: 1.0 Sent to CCL by: "zjwu" [zjwu:_:imr.edu] I appreaciate very much about the fruitful suggestions concerning my questions from Dr. Fan Huajun, Dr. Demetrios Xenides, Dr. Anastasios Papadopoulos, Dr. Douglas J. Fox and Dr. David Shobe. My question is: how to put f polarization effect in LANL2DZ calculation. The summary of the input file is as follows: #p b3lyp/gen gfinput pseudo=read opt scf(maxcycle=1024) Title Card Required 0 5 C W 1 R R 2.0 C 0 6-311++g(df) **** W 0 LANL2DZ F 1 1.00 .8230000000D+00 .1000000000D+01 **** W 0 LANL2DZ Cheers! Zhijian WU From owner-chemistry@ccl.net Fri Feb 3 19:09:00 2006 From: "Carsten Detering detering*_*biosolveit.de" To: CCL Subject: CCL: Ligand Docking with GOLD Message-Id: <-30782-060203183636-12422-lcEQVDIscp+vw5/pbAgWjQ%%server.ccl.net> X-Original-From: Carsten Detering Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 03 Feb 2006 23:40:21 +0100 MIME-Version: 1.0 Sent to CCL by: Carsten Detering [detering%%biosolveit.de] Hello Thomas, one article that comes to my mind is a study conducted by GSK: Warren et al A Critical Assessment of Docking Programs and Scoring Functions J.Med.Chem. ASAP article 2005 Hope this helps, Carsten ------------------------------------------------------------------ BioSolveIT GmbH - An der Ziegelei 75 - 53757 St.Augustin - Germany Dr. Carsten Detering detering%biosolveit.de Phone: +49-2241-2525-0 / Fax: -525 www.biosolveit.de Thomas Steinbrecher steinbrt^-^uni-freiburg.de schrieb: > Sent to CCL by: "Thomas Steinbrecher" [steinbrt[a]uni-freiburg.de] > Dear CCLers, > > can somebody point me to a review article that compares the performance of the GOLD ligand docking program to other commonly available docking tools like FlexX, AutoDock etc. ? > > Kind Regards, > > Thomas Steinbrecher > > >