From chemistry-request@server.ccl.net Fri Nov 17 01:18:02 2000 Received: from kuku.excite.com (kuku-rwcmta.excite.com [198.3.99.63]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA27782 for ; Fri, 17 Nov 2000 01:18:02 -0500 Received: from prance.excite.com ([199.172.153.84]) by kuku.excite.com (InterMail vM.4.01.02.39 201-229-119-122) with ESMTP id <20001117061555.VHK13249.kuku.excite.com@prance.excite.com> for ; Thu, 16 Nov 2000 22:15:55 -0800 Message-ID: <30158675.974441755012.JavaMail.imail@prance.excite.com> Date: Thu, 16 Nov 2000 22:15:55 -0800 (PST) From: Zilvinas Rinkevicius To: chemistry@ccl.net Subject: Erbium basis set Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Excite Inbox X-Sender-Ip: 193.219.34.90 Dear CCL users, I looking for medium size basis without ECP for Erbium. I obtained WTBS basis from Gaussian basis set library, but this basis to big for my aplications. Thanking in advance, Zilvinas Rinkevicius, Kaunas Technology University, Faculty of Fundamental Sciences, Studentu st. 50, Kaunas 3000, Lithuania. _______________________________________________________ Tired of slow Internet? Get @Home Broadband Internet http://www.home.com/xinbox/signup.html From chemistry-request@server.ccl.net Fri Nov 17 03:29:52 2000 Received: from mail2.netcologne.de (mail2.netcologne.de [194.8.194.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA28318 for ; Fri, 17 Nov 2000 03:29:52 -0500 Received: from cosmologic.de (dial-194-8-209-157.netcologne.de [194.8.209.157]) by mail2.netcologne.de (8.9.3/8.9.3) with ESMTP id JAA23465; Fri, 17 Nov 2000 09:29:21 +0100 (MET) Message-ID: <3A0D4EF0.C6295361@cosmologic.de> Date: Sat, 11 Nov 2000 14:51:44 +0100 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (Win98; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: "Bruce. Tattershall" CC: "Phillip D. Matz" , Ji Hai-tao , chemistry@ccl.net Subject: Re: CCL:conformer population References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Bruce, I am Andreas Klamt, the author of the solvation models COSMO and COSMO-RS. To my experience, the change in vibrational free energies due to solvation is small, or at least it is usually a small contribution hidden within the non-electrostatic terms in continuum solvation models. Thus it does not appear necessary to calculate frequencies in solution explicitely (which by the way is not trivial). Within our COSMO-RS method (available as software COSMOtherm from COSMOlogic) we typically just calculate the total electronic energy of the conformers in a conductor add the chemical potential of the conformer in a solvent (relative to conductor), as calculated by COSMOtherm. Honestly spoken, we just forget about zero point vibrations a his place. This appears to work very well. In a recent blind-test on conformational free energies of polyionic cyclic amino-acids in water COSMOtherm performed by far best. We had an rms of about 2.2 kJ/mol. Note, that this is for poly-ions. For neutral structures there is goog hope to be even more accurate. ["Conformational analysis of cyclic acidic a-amino acids in aqueous solution - an evaluation of different continuum hydration models." Peter Aadal Nielsen, Per-Ola Norrby, Jerzy W. Jaroszewski, and Tommy Liljefors, manuscript, to be published] Sincerely Andreas P.S.: We just got COSMOtherm running with Gaussian COSMO-calculations. The respective sub-release of Gaussian will be available soon, hopefully. -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Nov 17 06:20:54 2000 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA29526 for ; Fri, 17 Nov 2000 06:20:53 -0500 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id MAA22733 for ; Fri, 17 Nov 2000 12:20:33 +0100 (MET) Date: Fri, 17 Nov 2000 12:20:33 +0100 (MET) Message-Id: <200011171120.MAA22733@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: help with Hyperchem constrain bond length Hi, I would like to perform a full optimization using a semiempirical method with Hyperchem except for one parameter (bond length). What I did is the following: - I've selected the bond - I named it (other: bond) - I've set a different bond length (set bond length) - I've constrained the bond length - I've deselected the bond (otherwise an error message appears) - I've run the optimization In the end of the optimization the bond length is optimized again giving the message: bond distance atom 8 to 7 is 1.44... A (build to 1.42... A). Can anyone give me a hint about what I'm doing wrong ? Thanks in advance. I will summarize .. Sergiusz ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Fri Nov 17 06:24:23 2000 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA29573 for ; Fri, 17 Nov 2000 06:24:23 -0500 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id MAA28762; Fri, 17 Nov 2000 12:23:43 +0100 (MET) Date: Fri, 17 Nov 2000 12:23:43 +0100 (MET) Message-Id: <200011171123.MAA28762@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: "art'" From: sergiusz kwasniewski Subject: Re: CCL:UHF vs. ROHF ??? Cc: CCL Hi, as far as I remember with ROHF you don't make a difference between alpha-MO's and beta-MO's. But it enables you to have one or more unpaired electrons put in the highest bonding MO's/lowest virtual MO's. UHF on the other hand distinguishes alpha and beta-MO's for all MO's. Hope this helps.. Sergiusz ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Thu Nov 16 14:06:07 2000 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA24208 for ; Thu, 16 Nov 2000 14:06:07 -0500 Received: from cornell.edu (phobos.mbg.cornell.edu [128.84.203.151]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id OAA25946; Thu, 16 Nov 2000 14:05:48 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3A1430A5.12EAC893@cornell.edu> Date: Thu, 16 Nov 2000 14:08:21 -0500 From: Richard Gillilan Reply-To: reg8@cornell.edu X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16-3 i686) X-Accept-Language: en MIME-Version: 1.0 CC: CCL , sm114@cornell.edu Subject: Autodock accept/reject ratio References: <3A12DB39.DC7EDB55@ccc.uni-erlangen.de> <004d01c04fac$c19f84c0$204f959f@farma.unimi.it.farma.unimi.it> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I'm trying to do an Autodock S.A. run on a ligand (simple chain with 13 torsions) and a small protein. I know the binding mode of the ligand from the x-ray structure, so this is really just a test. The setup scripts seem to work fine. Grid files and are centered on the ligand by default and extend well beyond the binding pocket (which is buried). When I do a series of simulated annealing runs with the default parameters the program does locate conformations, but there is no good clustering anywhere and the Acc/Rej ratio is tiny (<0.03) and often zero. I suspect I'm not getting a good sampling of the conformational space. I've tried increasing the accs and rejs variables (from 100 to 1000) and also made tstep,qstep and dstep small (from 2.0A to 0.2A and from 50 deg to .5 deg), but no luck .... Acc/Rej is still small. If I understand correctly, this ratio should be more like 30%. Anyone recognize the problem? Richard Gillilan MacCHESS/MBG Cornell University A few lines of the log file: Minimum Average | Acc/ Accepted: Rejected: | | XYZ-Translation | Run: Cycle: Energy: Energy: | /Rej: Down: Up: Total: Edge: | RT: | of Min.Energy | 1 /10 1 /50 +1.24 +1.24 0.00 0 0 1000 758 616.0 13.54 36.27 -0.29 1 /10 2 /50 +1.24 +1.24 0.00 0 0 1000 794 603.7 13.54 36.27 -0.29 1 /10 3 /50 -0.03 +2.62 0.00 1 1 1000 748 591.4 13.55 36.27 -0.28 1 /10 4 /50 -0.03 +2.11 0.00 0 1 1000 786 579.0 13.55 36.27 -0.28 1 /10 5 /50 -0.03 +85.63 0.00 1 1 1000 786 566.7 13.55 36.27 -0.28 From chemistry-request@server.ccl.net Thu Nov 16 18:34:56 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA26101 for ; Thu, 16 Nov 2000 18:34:55 -0500 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id PAA26545; Thu, 16 Nov 2000 15:34:56 -0800 (PST) Received: from 40dhcp41.msi.com(146.202.40.193) by mailhost.msi.com via smap (V2.0) id xma026539; Thu, 16 Nov 00 15:34:53 -0800 Message-Id: <4.2.0.58.20001116151909.00a9d420@146.202.6.218> X-Sender: nxt@146.202.6.218 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Thu, 16 Nov 2000 15:24:05 -0800 To: chemistry@ccl.net From: Noppawan Tanpipat Subject: Re: CCL:Analysing DMOL dos files in Cerius2 Cc: "Dr. Klaus Stark" , Stefan Bromley In-Reply-To: <3.0.32.20001116150448.00998e90@mailhost.munich.msi-eu.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear All, A minor addition to the email MSI's Klaus Stark sent below, the program "pdos" which converts *.dos files into *.grf files which can then be read by Cerius2 in 'Tables and Graphs', can be obtained by contacting "support@msi.com". Best wishes, Noppawan Tanpipat MSI At 03:04 PM 11/16/00 -0600, Dr. Klaus Stark wrote: >Dear All, > >please note that this is a web page for members of MSI's >Catalysis2000 Consortium only. It is password protected and not >generally accessible. > >Best regards > >Klaus Stark > >At 01:06 PM 11/16/00 +0000, Stefan Bromley wrote: > >Hi all, > > > >For anyone having also having trouble with analysing *.dos files in > >Cerius2 I have had been informed of the following solution: > > > >The current vesion of the Cerius2 does not actually support > >reading/analysing DOS files from DMOL3. To do so you have to look for > >"Displaying DMol partial density of states" at: > > > >http://www.msi.com/user/consortia/catalysis/Script/scipts.html > > > >Here a program can be found "pdos" which converts *.dos files into *.grf > >files which can then be read by Cerius2 in 'Tables and Graphs'. > > > >Stefan > > > > > > > >********************************************************************** > >This email and any files transmitted with it are confidential and > >intended solely for the use of the individual or entity to whom they > >are addressed. If you have received this email in error please notify > >the system manager. > > > >This footnote also confirms that this email message has been swept by > >MIMEsweeper for the presence of computer viruses. > > > >www.mimesweeper.com > >********************************************************************** > > > >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins > > > > > > > > > > >-- >Dr. Klaus Stark >Application Scientist >Molecular Simulations Inc. >Inselkammerstr. 1 >82 008 Unterhaching >Germany > >Phone : ++49-89-61459-420 >Mobile : ++49-172-936-3380 >Fax : ++49-89-61459-400 >E-Mail : kstark@msi.de >Web Page : http://www.msi.com > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > From chemistry-request@server.ccl.net Fri Nov 17 03:51:07 2000 Received: from cheviot1.ncl.ac.uk (root@cheviot1.ncl.ac.uk [128.240.233.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA28440 for ; Fri, 17 Nov 2000 03:51:07 -0500 Received: from aidan.ncl.ac.uk (nbwt@aidan.ncl.ac.uk [128.240.233.1]) by cheviot1.ncl.ac.uk (8.10.1/8.10.1) with ESMTP id eAH8ovM28422; Fri, 17 Nov 2000 08:50:57 GMT Received: from localhost (nbwt@localhost) by aidan.ncl.ac.uk (8.9.3+Sun/8.9.0) with ESMTP id IAA01041; Fri, 17 Nov 2000 08:50:57 GMT X-Authentication-Warning: aidan.ncl.ac.uk: nbwt owned process doing -bs Date: Fri, 17 Nov 2000 08:50:57 +0000 (GMT) From: "Bruce. Tattershall" X-Sender: nbwt@aidan.ncl.ac.uk To: "Dr. Andreas Klamt" cc: "Phillip D. Matz" , Ji Hai-tao , chemistry@ccl.net Subject: Re: CCL:conformer population In-Reply-To: <3A0D4EF0.C6295361@cosmologic.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Filter-Version: 1.8 (cheviot1.ncl.ac.uk) Thank you very much for your informative email. Very few others have replied, which I found quite surprising, considering how many people must make use of this kind of calculation. Bruce From chemistry-request@server.ccl.net Fri Nov 17 05:15:14 2000 Received: from lithium.theochem.uni-duesseldorf.de (lithium.theochem.uni-duesseldorf.de [134.99.82.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA29011 for ; Fri, 17 Nov 2000 05:15:11 -0500 Received: from borussia.theochem.uni-duesseldorf.de (borussia.theochem.uni-duesseldorf.de [134.99.82.13]) by lithium.theochem.uni-duesseldorf.de (8.11.1/8.11.1) with ESMTP id eAHADFi20469; Fri, 17 Nov 2000 11:13:15 +0100 Received: from localhost (localhost [[UNIX: localhost]]) by borussia.theochem.uni-duesseldorf.de (8.11.1/8.11.1) id eAHAD5N02396; Fri, 17 Nov 2000 11:13:05 +0100 From: Wibke Sudholt Reply-To: wibke@theochem.uni-duesseldorf.de To: chemistry@ccl.net Subject: SUMMARY: Excited State Reviews Date: Fri, 17 Nov 2000 10:19:02 +0100 X-Mailer: KMail [version 1.0.29] Content-Type: text/plain Cc: jbaudry@ttpharma.com, adolfas.gaigalas@nist.gov, tapaskar@cc.usu.edu, sergiusz.kwasniewski@luc.ac.be, elewars@trentu.ca, lipkowitz@chem.iupui.edu, mdt26@phy.cam.ac.uk, grimmes@uni-muenster.de, depaz@uam.es, jkerkin@cc.uoa.gr, kyiwong@phy.cuhk.edu.hk, qtccl@gala.net MIME-Version: 1.0 Message-Id: <00111711130500.02253@borussia> Content-Transfer-Encoding: 8bit Hello CCLers, I was asked to provide a summary of the answers to my question regarding reviews of excited electronic state calculations. So, here it is! I have to thank very much (in alphabetical order; hopefully, I did not forget to mention anybody) ... Jerome Baudry Adolfas Gaigalas Tapas Kar Sergiusz Kwasniewski E. Lewars Kenny Lipkowitz Michael Towler ... for sending answers to my question! Stefan Grimme ... for sharing some private information! Jose Luis Garcia de Paz Ioannis Kerkines Kiniu Wong Kin-Yiu Qadir K. Timerghazin ... for their interest in a summary! I was also asked about the references for DFT/SCI and DFT/MRCI: S. Grimme, Density functional calculations with configuration interaction for the excited states of molecules, Chem. Phys. Lett., 259, (1996), 128 S. Grimme und M. Waletzke, A Combination of Kohn-Sham Density Functional Theory and Multi-Reference Configuration Interaction Methods, J. Chem. Phys., 111, (1999), 5645 In addition, please take a look at: http://www.uni-muenster.de/Chemie/OC/research/grimme/1publ.html Best regards Wibke Sudholt Institute of Theoretical Chemistry Heinrich-Heine-University Duesseldorf, Germany wibke@theochem.uni-duesseldorf.de ***** Original Question ***** Dear CCLers, I'm looking for review papers and/or key articles and/or web pages about the quantum chemical calculation of electronically excited states (especially singlet excited states). I'm interested in organic molecules with about 10 heavy atoms (about 20 atoms in total). The question I would like to answer is: Which semiempirical/ab initio/density functional methods are known for this purpose? How expensive and accurate are they? I'm aware of the CASSCF/CASPT2 articles of Roos et al. and also of some papers about CIS, TDDFT, DFT/SCI and DFT/MRCI. Thank you very much in advance! Best regards Wibke Sudholt Institute of Theoretical Chemistry Heinrich-Heine-University Duesseldorf, Germany wibke@theochem.uni-duesseldorf.de ***** Answers ***** Dear Wibke You can have a look at: Characterization of a Conical Intersection between the Ground and First Excited State for a Retinal Analog. Ferenc Molnar, Michal Ben-Nun, Todd J. Martínez, and Klaus Schulten. Journal of Molecular Structure (THEOCHEM), WATOC special issue, 506:169--178, 2000. abstract visible at: http://www.ks.uiuc.edu/Publications/Papers/abstract.cgi?tbcode=MOLN2000A Hope it helps, Cheers ***************************************** Jerome Baudry, Ph.D. Research Scientist, Computational Chemistry TransTech Pharma, Inc. 4170 Mendenhall Oaks Pwky, Suite 110 High Point, NC, 27265 http://www.ttpharma.com jbaudry@ttpharma.com tel: (336) 841-0300 #120 fax: (336) 841-0310 *************** Dear Dr. Sudholt, We( at NIST,USA) are also interested in calculating excited S states of organic molecules(e.g. fluorescein). Arvydas Tamulis has been trying to do these calculations for us. He may be able to tell you about his experience. Below is his address. tamulis@itpa.lt Arvydas Tamulis Institute of Theoretical Physics and Astronomy, Theoretical Molecular Electronics Research Group, A. Gostauto 12, Vilnius 2600, Lithuania e-mail: TAMULIS@ITPA.lt; WEBsite: http://www.itpa.lt/~tamulis/ fax: +(370-2)-225361 or +(370-2)-224694 Phone: +(370-2)-620861 < some private information cuted out > Please keep me informed about your efforts. My understanding is that these calculations are difficult and on the forefront of what is possible. Adolfas Gaigalas *************** Hi, Here is the paper which might be helpful. Comparison of methods for calculating the properties of intramolecular hydrogen bonds. excited state proton transfer. T. Kar, S. Scheiner and M, Cuma, J. Chem. Phys., 111 (1999) 849-858. Tapas ______________________________________ Tapas Kar, Ph.D Department of Chemistry & Biochemistry Utah State University 0300 Old Main Hill Logan, UT 84322-0300 Voice: 435-797-7230 Fax: 435-797-3390 Email: tapaskar@cc.usu.edu tapas@risky3.chem.usu.edu *************** Hi, A frequently used semiempirical method is Zerners ZINDO/S in combi with CIS. It provides quite accurate one electron excitation energies for amongst others organic molecules. All calculated excitations belong to valence transitions however. If you're planning to include calculation of rydberg states as well then you should focus on ab initio methods like CASPT2, CCSD(T) and TDDFT. ref for ZINDO/S: MC Zerner, GH Loew, RF Kirchner, UT Mueller-Westerhoff, JACS, 1980, 102, 589 GM Pearl, MC Zerner, A Broo, J McKelvey, J Comp Chem, 1998, 19, 781 Hope that this is usefull and that you'll send a summary to CCL. Bye Sergiusz ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ *************** W. Sudholt asked for the calc of electronic excited states: Hello, Good results for electronically excited states are often obtained from ZINDO/S, a semiempirical method (fast), and from time-dependent DFT (DDFT) (much slower). Another standard method is RCIS. I think ZINDO/S and TDDFT are best. All three are available in Gaussian 98. I could send you some typical input files. ZINDO/S is a version of INDO/S (M. Kotzian, N. Rosch, and M. C. Zerner, Theor Chim Acta, 1992, 81, 201) developed by the group of the late Michael Zerner (hence Z). TDDFT: M. E. Casida in "Recent developments and applications of modern density functional theory", J. M. Seminario, Ed., Elsevier, Amsterdam, 1996 and refs therein. R. E. Stratmen et al, J Chem Phys, 1998, 109, 8218. K. B. Wiberg e al, Chem Phys Lett, 1998, 297, 60 RCIS J. B. Foresman and A. Frisch, "Exploring Chemistry..." Gaussian Inc, Pittsburgh, PA, 1996, p. 218. E. Lewars *************** A chapter by Michael Robb (first author) entitled "Computational Strategy for Organic Photochemistry" has been published in Reviews in Computational Chemistry, vol. 15, 2000, Wiley VCH Publishers, K. Lipkowitz and D. Boyd, eds., pp 87-147. This may be of value to you. Kenny Lipkowitz *************** Hello Wibke, Quantum Monte Carlo is probably the most accurate ab initio technique available for molecules of medium size and above. It is capable of treating excited states. For recent applications to molecular excited states, see: Excitons in small hydrogenated silicon clusters. A.R. Porter, M.D. Towler and R.J. Needs Electronic excited-state wave functions for quantum Monte Carlo: application to silane and methane A.R. Porter, O.K. Al-Mushadani, M.D. Towler and R.J. Needs These are available in preprint form from : www.tcm.phy.cam.ac.uk/~mdt26/casino.html Regards, Mike Towler ------------------------------------------------------------------------- Dr. Mike Towler (mdt26@phy.cam.ac.uk) Theory of Condensed Matter (Rm 537) Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK Tel. +44-(0)1223-337359 Fax. +44-(0)1223-337356 ----------------WWW: http://www.tcm.phy.cam.ac.uk/~mdt26/ --------------- From chemistry-request@server.ccl.net Fri Nov 17 07:56:43 2000 Received: from srvnt01.osmetech.plc.uk (aromascn.demon.co.uk [158.152.95.246]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA31121 for ; Fri, 17 Nov 2000 07:56:40 -0500 Received: by SRVNT01 with Internet Mail Service (5.0.1461.28) id ; Fri, 17 Nov 2000 12:49:38 -0000 Message-ID: <09433A5B7967D3119BE30090278D112321ADAF@SRVNT01> From: Tom Hawkins To: chemistry@ccl.net Cc: "'sergiusz kwasniewski'" Subject: RE: help with Hyperchem constrain bond length Date: Fri, 17 Nov 2000 12:49:37 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1461.28) Content-Type: text/plain; charset="iso-8859-1" sergiusz kwasniewski [mailto:sergiusz.kwasniewski@luc.ac.be] said: >I would like to perform a full optimization using a semiempirical method >with Hyperchem except for one parameter (bond length). (...) >In the end of the optimization the bond length is optimized again giving >the message: bond distance atom 8 to 7 is 1.44... A (build to 1.42... A). To fix a parameter during optimisation you need to use a Restraint (in Hyperchem's Setup menu). The Constraint items in the Build menu only apply to model building, not to optimisation. If you are using a restraint and the bond length is still changing, maybe you need to give the restraint a higher force constant. The Hyperchem manual says the default force constants are chosen for molecular dynamics work and may need increasing for geometry optimisation. Restraints are covered on page 224 of the Hyperchem 5 reference manual and page 203 of the computational chemistry manual. Make sure to read the note about energy calculations when using restraints. Hope this helps Dr Tom Hawkins Osmetech plc Sensor Technologist Electra House, Electra Way, Crewe CW1 6WZ thawkins@osmetech.plc.uk Tel +44(0)1270 216444 Fax +44(0)1270 216030 From chemistry-request@server.ccl.net Fri Nov 17 09:09:27 2000 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA31662 for ; Fri, 17 Nov 2000 09:09:25 -0500 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id PAA20565 for ; Fri, 17 Nov 2000 15:09:03 +0100 (MET) Date: Fri, 17 Nov 2000 15:09:03 +0100 (MET) Message-Id: <200011171409.PAA20565@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: Summary: help with Hyperchem constrain bond length Hi, thanks to your help the problem seems to be overcome. What I finally did is I REstrained (not constrained) the bond to a particular value and gave it a high force constant. The restraint value changes a bit but stays in the margin that I consider to be useful in this case.. So thanks for all your help ! Here are the responses: Hi Sergiusz try the following - select de bond - set the bond length - do a complement selection (menu Select/Complement selection) - run the optimization if an error occurs, try first to optimize with another method (i.e. MM+) first and/or change the optimization Algorithm. Hope it helps Jordi Teixido XXXXXXXXXXXXXXX Hi Sergiusz, I am afraid I don't know how to keep a bond length fixed with HyperChem (I don't have access to the program anymore), but from what I remember, the "constrain bond length" option in the Build menu just sets the initial value i.e., it does not fix it. I agree that the term "constrain" is misleading. Best wishes, Tanja van Mourik XXXXXXXXXXXXXXX Hi The constraint is only a 'constraint' not absolute. It has a high energy for distortion but may be distorted. You can increase the energy for distortion but you can not make it infinite. you always will get a small change therefore. Best wishes Martin Chaplin XXXXXXXXXXXXXXX To fix a parameter during optimisation you need to use a Restraint (in Hyperchem's Setup menu). The Constraint items in the Build menu only apply to model building, not to optimisation. If you are using a restraint and the bond length is still changing, maybe you need to give the restraint a higher force constant. The Hyperchem manual says the default force constants are chosen for molecular dynamics work and may need increasing for geometry optimisation. Restraints are covered on page 224 of the Hyperchem 5 reference manual and page 203 of the computational chemistry manual. Make sure to read the note about energy calculations when using restraints. Hope this helps Tom Hawkins XXXXXXXXXXXXXXX Dear Sergiusz, first of all be aware of HyperChem's differentiation between constraint (Molcular builder, build-menu) and restraint (chemical calculations, setup menu ). To restrain the selected bond length you must change the Force Constant Value in the Restrained Forces Dialog Box to a much larger number (e.g. 5000 - 10000). The Default value (7) is inappropriate for a restrained geometry optimization. Lutz Prue XXXXXXXXXXXXXXX ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Fri Nov 17 08:27:36 2000 Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA31316 for ; Fri, 17 Nov 2000 08:27:34 -0500 Received: from gotham.ccc.nottingham.ac.uk ([128.243.40.48] helo=unix.ccc.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.16 #1) id 13wlX6-0004Yg-00; Fri, 17 Nov 2000 13:26:24 +0000 Received: from granby ([128.243.40.43] helo=granby.ccc.nottingham.ac.uk) by unix.ccc.nottingham.ac.uk with esmtp (Exim 3.16 #1) id 13wlXg-0000nS-00; Fri, 17 Nov 2000 13:27:00 +0000 Date: Fri, 17 Nov 2000 13:26:59 +0000 (GMT) From: Simon Cross X-Sender: pcxsc@granby.ccc.nottingham.ac.uk To: Richard Gillilan cc: CCL , sm114@cornell.edu Subject: Re: CCL:Autodock accept/reject ratio In-Reply-To: <3A1430A5.12EAC893@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Surely if the binding pocket is buried, the ligand will have no way of making it into this pocket. This then means that you will get the ligand moving into local minima at the surface of the protein, but will then move away from these, explaining the lack of clustering. Even with antibodies, my small chemical hapten antigens could not get completely into the binding pocket which must have been in a 'half closed' conformation. I got reasonable clustering for this, although the differences in energy between clusters was minimal (default value). If you have the crystal structure and are just trying to test autodock then the benzothiazole example worked for me. Here the binding pocket is open and the benzothazole is small and rigid, so it works well. For your example, I suspect that it is just telling you that there is no good binding site to be found (due to it being buried). Hope this helps, Simon ----------------------------------------- Simon Cross School of Chemistry University of Nottingham tel. 0115 9514193 Email: pcxsc@nottingham.ac.uk On Thu, 16 Nov 2000, Richard Gillilan wrote: > I'm trying to do an Autodock S.A. run on a ligand (simple chain with > 13 torsions) and a small protein. I know the binding mode of the > ligand from the x-ray structure, so this is really just a test. The > setup scripts seem to work fine. Grid files and are centered on the > ligand by default and extend well beyond the binding pocket (which is > buried). When I do a series of simulated annealing runs with the > default parameters the program does locate conformations, but there is > no good clustering anywhere and the Acc/Rej ratio is tiny (<0.03) and > often zero. I suspect I'm not getting a good sampling of the > conformational space. I've tried increasing the accs and rejs > variables (from 100 to 1000) and also made tstep,qstep and dstep small > (from 2.0A to 0.2A and from 50 deg to .5 deg), but no luck .... > Acc/Rej is still small. If I understand correctly, this ratio should > be more like 30%. > > Anyone recognize the problem? > > Richard Gillilan > MacCHESS/MBG > Cornell University > > A few lines of the log file: > > Minimum Average | Acc/ Accepted: Rejected: | | > XYZ-Translation | Run: Cycle: Energy: Energy: | /Rej: Down: Up: > Total: Edge: | RT: | of Min.Energy | 1 /10 1 /50 +1.24 +1.24 0.00 0 > 0 1000 758 616.0 13.54 36.27 -0.29 1 /10 2 /50 +1.24 +1.24 0.00 0 0 > 1000 794 603.7 13.54 36.27 -0.29 1 /10 3 /50 -0.03 +2.62 0.00 1 1 1000 > 748 591.4 13.55 36.27 -0.28 1 /10 4 /50 -0.03 +2.11 0.00 0 1 1000 786 > 579.0 13.55 36.27 -0.28 1 /10 5 /50 -0.03 +85.63 0.00 1 1 1000 786 > 566.7 13.55 36.27 -0.28 > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Fri Nov 17 09:35:59 2000 Received: from mel.ruc.dk (mel.ruc.dk [130.225.220.27]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA31819 for ; Fri, 17 Nov 2000 09:35:58 -0500 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id PAA05522; Fri, 17 Nov 2000 15:35:44 +0100 (MET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id PAA02733; Fri, 17 Nov 2000 15:23:38 +0100 (MET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 17 Nov 00 15:35:44 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 17 Nov 00 15:35:39 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: sergiusz kwasniewski Date: Fri, 17 Nov 2000 15:35:37 +0100 Subject: Re: CCL:help with Hyperchem constrain bond length CC: chemistry@ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <29F001B1439@virgil.ruc.dk> Sergiusz Kwasniewski: > I would like to perform a full optimization using a semiempirical method > with Hyperchem except for one parameter (bond length). What I did is the > following: > > - I've selected the bond > - I named it (other: bond) > - I've set a different bond length (set bond length) > - I've constrained the bond length > - I've deselected the bond (otherwise an error message appears) > - I've run the optimization > > In the end of the optimization the bond length is optimized again giving > the message: bond distance atom 8 to 7 is 1.44... A (build to 1.42... A). > > Can anyone give me a hint about what I'm doing wrong ? Thanks in advance. I > will summarize .. The 'Restraints' tool in HyperChem is ingenious and useful, but it is essential to know how it works. The 'Set bond length' option in the 'Edit' menu does not constrain the bond length during geometry optimization. You must select the 'Setup' menu and enter the 'Restraints' option (you probably did that). Here you must activate the named selection, set the 'Restrained value' and the value of the 'Force constant'. When you now perform a calculation of molecular energy (by some of the available procedures), HyperChem adds the energy of a harmonic force field corresponding to the values set in 'Restraints'. The selected restraint "punishes" the molecule for adopting a geometrical parameter for the named selection that deviates from the 'restrained value', and a geometry optimization will tend to approach this value. However, the default value of the force constant parameter is only 7 kcal mol^-1 A^-2, which is a very soft restraint. If you want to fix the geometrical parameter efficiently, you must increase the value of the force constant. Try out a series of increasing values to get a feeling for the results. Maybe a restraint force constant of 1000 or 10000 is necessary to fix the bond length according to your wishes. After succesful geometry optimization, it is safest to perform a single point calculation without restraints to obtain the proper molecular energy. Good Luck! Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Fri Nov 17 10:08:35 2000 Received: from dogstar.duch.udel.edu (dogstar.duch.udel.edu [128.175.138.122]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA31949 for ; Fri, 17 Nov 2000 10:08:34 -0500 Received: from localhost (gijukt@localhost) by dogstar.duch.udel.edu (8.9.3/8.9.3) with ESMTP id KAA275293 for ; Fri, 17 Nov 2000 10:09:35 -0500 (EST) Date: Fri, 17 Nov 2000 10:09:34 -0500 From: Giju Thomas Kalathingal To: chemistry@ccl.net Subject: Summary:classical free energy Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, Recently I posted a question on "classical free energy of formation". Hereby I thankfully summarise those responses. Sincerely, Giju -------------------------------------------------------------------------------- Original Question was: Hi Everybody, Could you please give me some references or suggestions on how to estimate classical free energy of formation of a molecule? Thanks in advance, Giju -------------------------------------------------------------------------------- Dear Giju, >Hi Everybody, >Could you please give me some references or suggestions on how >to estimate classical free energy of formation of a molecule? >Thanks in advance, >Giju You will find some useful material in the chapter: L. A. Curtiss, P. C. Redfern, and D. J. Frurip, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 2000, Vol. 15, pp. 147-211. Theoretical Methods for Computing Enthalpies of Formation of Gaseous Compounds. Good luck, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu -------------------------------------------------------------------------------- Giju, GAt 05:22 PM 11/14/00 -0500, you wrote: >Could you please give me some references or suggestions on how >to estimate classical free energy of formation of a molecule? I don't see any reason this can't be done with the same free energy perturbation methods that are more commonly used for ligand-receptor binding and solvation free energies. It would be much easier, in fact, since there are no solvent modes to average over. The problem will be the quality of the force field you use. Chances are it will be of different (better) quality for the molecular species you are interested in than for the standard-state species (graphite/H2/O2/etc) that you will also need to use in your thermodynamic cycle. If you're looking for references on free energy perturbation in general, a good place to start is A. R. Leach, "Molecular Modelling", Chapter 9. There are many further references given there. On an unrelated note, I notice that you are at the University of Delaware. By coincidence, I will be there on Monday to give a seminar. Maybe we could talk then. -Steve Stuart ---------------- Steven J. Stuart Assistant Professor Department of Chemistry Clemson University Clemson, SC 29634-0973 (864)656-5013 (864)656-6613 (fax) http://radar.ces.clemson.edu -------------------------------------------------------------------------------- Hello! I think you are after Hess's Law of Heat Formation which is a way of obtaining the enthalpy of formation of a molecule. Respectfully, Phillip Matz matz@wsunix.wsu.edu -------------------------------------------------------------------------------- Hi Giju I was wondering if you would be kind enough to forward me your responses. I too am interested in the classical free energy. Thanks. **************************************************************** Benjamin J. Moritz home (602) 453-9411 Dept. of Chemistry & Biochemistry work (480) 965-8509 Arizona State University Mailto:bmoritz@asu.edu P. O. Box 871604 Tempe, AZ 85287-1604 **************************************************************** "Karma is justice without the satisfaction." -------------------------------------------------------------------------------- ____________________________________________________________ Giju T. Kalathingal Department of Chemistry and Biochemistry University of Delaware, Newark, Delaware 19716, USA. E-mail: gijukt@udel.edu URL: http://dogstar.duch.udel.edu/gijukt/welcome.html ____________________________________________________________ From chemistry-request@server.ccl.net Fri Nov 17 10:35:57 2000 Received: from aleph.net.uniovi.es (aleph.net.uniovi.es [156.35.11.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA32084 for ; Fri, 17 Nov 2000 10:35:57 -0500 Received: from pinon.ccu.uniovi.es (pinon.ccu.uniovi.es [156.35.31.1]) by aleph.net.uniovi.es (PMDF V6.0-24 #45227) with ESMTP id <01JWNJ4WX5VW003IAS@aleph.net.uniovi.es> for CHEMISTRY@ccl.net; Fri, 17 Nov 2000 16:33:41 +0100 (MET) Received: (from pueyo@localhost) by pinon.ccu.uniovi.es (8.9.2/8.9.2) id QAA28502 for CHEMISTRY@ccl.net; Fri, 17 Nov 2000 16:33:40 +0100 (MET) Date: Fri, 17 Nov 2000 16:33:40 +0100 (MET) From: Victor Lua~na Subject: silicon based organic chemistry To: CHEMISTRY@ccl.net Message-id: <200011171533.QAA28502@pinon.ccu.uniovi.es> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Dear CCL readers, I have become interesting in the old subject of a silicon-based organic chemistry. Whereas it is simple to find hundred of papers reporting and discussing Si containing compounds, I would like to ask for your help in finding a few authoritative articles or reviews discussing any of: 1) is it possible to build a complex silicon-hydrogen chemistry functionally equivalent to carbochemistry? 2) why silicon produces a very complex silicate chemistry but carbonates are much simpler and fewer? I will produce a summary with your answers. Thanks for your help, Victor Lua~na victor@fluor.quimica.uniovi.es