From chemistry-request@server.ccl.net Thu Oct 31 17:38:35 2002 Received: from sims.csuohio.edu ([137.148.5.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9VMcZf09440 for ; Thu, 31 Oct 2002 17:38:35 -0500 Received: from [137.148.208.106] (scifac208-106.dhcp.csuohio.edu [137.148.208.106]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0H4V00E9FAXMG5@sims.csuohio.edu> for chemistry@ccl.net; Thu, 31 Oct 2002 17:39:22 -0500 (EST) Date: Thu, 31 Oct 2002 17:38:18 -0500 From: Michael Tallhamer Subject: Good DFT Book To: chemistry@ccl.net Message-id: MIME-version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT User-Agent: Microsoft-Entourage/10.0.0.1309 I am a student looking to buy a book on DFT on a limited research budget and would like to know if there are any good books covering the topic of DFT > from basics through complex theory. Just a good all around reference book or text book would be great. Price is not so important but I just don't want to have to by many books. The Chemistry Department won't go for that. Thanks for all of your suggestions Michael Tallhamer Research Asst Department of Chemistry Cleveland State University E-mail: m.tallhamer@csuohio.edu From chemistry-request@server.ccl.net Thu Oct 31 19:20:34 2002 Received: from mxout3.cac.washington.edu ([140.142.32.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA10KYf19730 for ; Thu, 31 Oct 2002 19:20:34 -0500 Received: from mailscan-out1.cac.washington.edu (mailscan-out1.cac.washington.edu [140.142.32.17]) by mxout3.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.09) with SMTP id gA10KTxL023027 for ; Thu, 31 Oct 2002 16:20:29 -0800 Received: FROM smtp.washington.edu BY mailscan-out1.cac.washington.edu ; Thu Oct 31 16:20:29 2002 -0800 Received: from donald ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW01.12/8.12.1+UW02.08) with SMTP id gA10KSZh013171 for ; Thu, 31 Oct 2002 16:20:28 -0800 Message-ID: <014d01c2813c$18ff7190$74805f80@donald> From: "Carsten Detering" To: Subject: autodock and database docking Date: Fri, 1 Nov 2002 01:17:43 +0100 Organization: University of Washington MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_014A_01C28144.7AB00370" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_014A_01C28144.7AB00370 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CClers, I am interested in docking a small (500-1000 molecules) database with = AutoDock. Is the program capable of doing that?? Has anyone got some = experience with that?? Thanks for helpful comments, Carsten ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Phone 206-543-5081 Fax 206-685-8665 email detering@u.washington.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------=_NextPart_000_014A_01C28144.7AB00370 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear CClers,

I am interested in docking a small (500-1000 molecules) database = with=20 AutoDock. Is the program capable of doing that?? Has anyone = got some=20 experience with that??

Thanks for helpful comments,

Carsten

~~~~~~~~~~~~~~~~~~~~~~~~~~~
Carsten Detering, = Ph.D.
University of=20 Washington
Seattle, WA 98195
Phone 206-543-5081
Fax=20 206-685-8665
email detering@u.washington.edu~~~~~~~~~~~~~~~~~~~~~~~~~~~

------=_NextPart_000_014A_01C28144.7AB00370-- From chemistry-request@server.ccl.net Thu Oct 31 19:43:44 2002 Received: from hotmail.com ([64.4.21.139]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA10hif21562 for ; Thu, 31 Oct 2002 19:43:44 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 31 Oct 2002 16:43:44 -0800 Received: from 137.189.4.4 by lw14fd.law14.hotmail.msn.com with HTTP; Fri, 01 Nov 2002 00:43:44 GMT X-Originating-IP: [137.189.4.4] From: "Wing Lok Abe Kurtz Chiu" To: janap@ncbr.chemi.muni.cz, chemistry@ccl.net Subject: Re: CCL:freezing heavy atoms, unfreezing hydrogens Date: Fri, 01 Nov 2002 08:43:44 +0800 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 01 Nov 2002 00:43:44.0898 (UTC) FILETIME=[BB882620:01C2813F] Hi, Simply carry out as the following example, put the freezed atoms in the section of Constants, then it will be OK. 0 1 N x1 y1 z1 C x2 y2 z2 H x3 y3 z3 N x4 y1 z4 C x5 y5 z5 H x6 y6 z6 Variables x3=0.000000 y3=0.000000 z3=0.648267 x6=0.000000 y6=0.000000 z6=-3.787082 Constants x1=0.000000 y1=0.000000 z1=2.873155 x2=0.000000 y2=0.000000 z2=1.723403 x4=0.000000 y4=0.000000 z4=-1.571503 x5=0.000000 y5=0.000000 z5=-2.718861 Cheers, Kurtz Dr. Wing Lok Abe Kurtz Chiu Department of Chemistry The Chinese University of Hong Kong Hong Kong SAR China >From: Jana Precechtelova >To: "CCL.NET" >Subject: CCL:freezing heavy atoms, unfreezing hydrogens >Date: Thu, 31 Oct 2002 18:02:28 +0100 (MET) > > >I`d like to perform a geometry optimization (in Gaussian) of a molecule >defined by cartesian coordinates. During the optimization, I need to >freeze heavy atoms but let hydrogens to be optimized. How can I easily >achieve this? I`ve already tried it using a ModRedundant option to the >Opt keyword and by specifying atoms to be fixed via this sequence: >X N F (N is a number of atom) but this attempt failed. > >Best regards, >Jana Precechtelova > > > >-------------------------------------------------------------------------- >Jana Precechtelova >National Centre for Biomolecular Research (NCBR) >Faculty of Science >Masaryk University >Kotlarska 2 email: janap@ncbr.chemi.muni.cz >611 37 Brno phone: +420-5-41129588 >The Czech Republic fax: +420-5-411 29 506 >-------------------------------------------------------------------------- > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: >jkl@ccl.net _________________________________________________________________ Choose an Internet access plan right for you -- try MSN! http://resourcecenter.msn.com/access/plans/default.asp From chemistry-request@server.ccl.net Fri Nov 1 02:35:43 2002 Received: from century.fen.bilkent.edu.tr ([139.179.97.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA17Zgf31686 for ; Fri, 1 Nov 2002 02:35:42 -0500 Received: from fen.bilkent.edu.tr (fenII-121.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id JAA22208 for ; Fri, 1 Nov 2002 09:30:45 +0200 (EET) Message-ID: <3DC22F78.5060705@fen.bilkent.edu.tr> Date: Fri, 01 Nov 2002 09:38:32 +0200 From: Ulrike Salzner Organization: Bilkent University User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:0.9.4) Gecko/20011128 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: polyene spectra Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello, in the literature it is commonly stated that UV absorbtion energies of polyenes with increasing chain lengths decrease approximately linearly when plotted against 1/n, the number of repeat units. Does anyone know where this has been stated for the first time and at which level of theory this is true exactly. I am writing a paper and I want to give a proper reference, however, usually people do not give a citation or they just cite their own previous papers. I suspect that the relationship does not necessarily hold when higher levels of theory are used and when the geometries are optimized. Can somebody comment on this? Thanks in advance, Ulrike Salzner From chemistry-request@server.ccl.net Fri Nov 1 06:00:00 2002 Received: from hotmail.com ([64.4.19.29]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA1B00f04670 for ; Fri, 1 Nov 2002 06:00:00 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 1 Nov 2002 02:59:59 -0800 Received: from 129.173.17.185 by lw12fd.law12.hotmail.msn.com with HTTP; Fri, 01 Nov 2002 10:59:59 GMT X-Originating-IP: [129.173.17.185] From: "Zhijian Wu" To: chemistry@ccl.net Subject: EA calculation Date: Fri, 01 Nov 2002 05:59:59 -0500 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 01 Nov 2002 10:59:59.0801 (UTC) FILETIME=[D24A9A90:01C28195]

Dear cclers,

I am trying to calculate the EA of a cluster. However, I found negative charged cluster is saddle points (with one or more imaginary frequences), the neutral cluster is a local minimum (without imaginary frequences). In this case, is it meaningful to calculate EA?

Thanks.

----------------

Zhijian WU, Ph.d

Department of Chemistry

Dalhousie University

Halifax, NS

Canada B3H 4J3

Get faster connections -- switch to MSN Internet Access! Click Here From chemistry-request@server.ccl.net Fri Nov 1 07:03:45 2002 Received: from fepB.post.tele.dk ([195.41.46.145]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA1C3jf06091 for ; Fri, 1 Nov 2002 07:03:45 -0500 Received: from cortex-xp02.cc.dk ([62.242.210.146]) by fepB.post.tele.dk (InterMail vM.4.01.03.23 201-229-121-123-20010418) with ESMTP id <20021101120344.USZC839.fepB.post.tele.dk@cortex-xp02.cc.dk> for ; Fri, 1 Nov 2002 13:03:44 +0100 Date: Fri, 1 Nov 2002 13:00:38 +0100 (CET) From: Kenneth Geisshirt Sender: kneth@lithium Reply-To: kenneth@geisshirt.dk To: ccl Subject: Re: CCL:Glycosylation & Phosphorylation In-Reply-To: <3DC12B72.7090705@health.nb.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=iso-8859-1 Content-Transfer-Encoding: 8BIT On Thu, 31 Oct 2002, Miroslava Cuperlovic-Culf wrote: > I would like to find out more about theoretical methods for studying > glycosilation and phosphorylation of proteins. Are there any programs > (ideally free) for prediction, modelling of it. You should take a look at http://www.cbs.dtu.dk/services/ - you will find a few prediction services in the area you're asking about. Kneth -- Kenneth Geisshirt, M.Sc., Ph.D. http://kenneth.geisshirt.dk Grøndals Parkvej 2A, 3. sal kenneth@geisshirt.dk DK-2720 Vanløse +45 38 87 78 38 From chemistry-request@server.ccl.net Fri Nov 1 02:55:43 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA17thf32376 for ; Fri, 1 Nov 2002 02:55:43 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id gA17tgb13709; Fri, 1 Nov 2002 02:55:42 -0500 (EST) Date: Fri, 1 Nov 2002 02:55:43 -0500 (EST) From: Jan Labanowski To: Michael Tallhamer cc: chemistry@ccl.net Subject: Re: Good DFT Book In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII For starters, you cannot beat the: A Chemist's Guide to Density Functional Theory Wolfram Koch, Max C. Holthausen, Wiley-VCH, Weinheim, 2001, ISBN 3-527-30372-3 (softcover) Used is about 50 on amazon.com Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | E-mail: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/~jkl Columbus, OH 43212-1163 | http://www.ccl.net/ http://asdn.net/ On Thu, 31 Oct 2002, Michael Tallhamer wrote: > Date: Thu, 31 Oct 2002 17:38:18 -0500 > From: Michael Tallhamer > To: chemistry@ccl.net > Subject: Good DFT Book > > I am a student looking to buy a book on DFT on a limited research budget > and would like to know if there are any good books covering the topic of DFT > from basics through complex theory. Just a good all around reference book or > text book would be great. Price is not so important but I just don't want to > have to by many books. The Chemistry Department won't go for that. > > Thanks for all of your suggestions > > Michael Tallhamer > Research Asst > Department of Chemistry > Cleveland State University > E-mail: m.tallhamer@csuohio.edu > From chemistry-request@server.ccl.net Fri Nov 1 02:44:58 2002 Received: from smtp01.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA17ivf31926 for ; Fri, 1 Nov 2002 02:44:57 -0500 Received: from PC12 (unknown [202.127.19.236]) by smtp01.sohu.com (Postfix) with ESMTP id 91D5D53656 for ; Fri, 1 Nov 2002 15:20:23 +0800 (CST) Date: Fri, 1 Nov 2002 15:46:39 +0800 From: "zgleo" To: "CHEMISTRY@ccl.net" Subject: Sybyl question X-mailer: Foxmail 4.1 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon180235483567_=====" Message-Id: <20021101072023.91D5D53656@smtp01.sohu.com> This is a multi-part message in MIME format. --=====000_Dragon180235483567_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear CCLers, I find a strange problem when I use sybyl. I plan to prepare some ligands for autodock. The first thing I have to do is to move these ligands to the pocket area of the receptor. So I read the receptor molecule and ligand molecule into D1 and D2,respectively. Then I move the ligand to the pocket area by focusing mouse on D2,and then save it as "ligand.mol2"(Didn't freeze view). After this,I zap the D2 and read "ligand.mol2" into D2. It looks that everything is OK----the ligand molecule is exactly in the pocket. Unfortunately,when I zap everything and read "ligand.mol2" into sybyl firstly and receptor file into sybyl subsequently,I find the ligand is located far away from the receptor. Then I change the order again----that is reading the receptor first and the ligand second,to my surprise,the ligand is located in the pocket area again. I'm completely confused by it. Does anybody know why? Thanks. 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SURFTlRJVFkNCkNyZWF0ZWQgb3IgbW9kaWZpZWQgYnkNCkVEIVNPTiAnOTYgW1hmL1VDZl0NCgA7 --=====000_Dragon180235483567_=====-- From chemistry-request@server.ccl.net Fri Nov 1 10:06:15 2002 Received: from brass.metals.hope.edu ([198.110.98.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gA1F6Ff09854 for ; Fri, 1 Nov 2002 10:06:15 -0500 Received: from hope.edu ([198.110.98.17]) by brass.metals.hope.edu (NAVGW 2.5.2.11) with SMTP id M2002110110061806469 ; Fri, 01 Nov 2002 10:06:18 -0500 Received: from [198.110.101.2] (polik@hope.edu) by hope.edu; Fri, 1 Nov 2002 10:06:17 -0500 X-WM-Posted-At: hope.edu; Fri, 1 Nov 02 10:06:17 -0500 Message-Id: <5.1.0.14.2.20021101095918.01f61510@webmail.hope.edu> X-Sender: polik@webmail.hope.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 01 Nov 2002 10:04:28 -0500 To: Ulrike Salzner From: "William F. Polik" Subject: Re: CCL:polyene spectra Cc: CHEMISTRY@ccl.net In-Reply-To: <3DC22F78.5060705@fen.bilkent.edu.tr> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Ulrike, This is a very common physical chemistry experiment illustrating the Particle-in-a-Box that is described in most physical chemistry laboratory textbooks, as well as in several articles in the Journal of Chemical education over the last decade. You can find several references to the older literature in Chapter 11 of Jaffe & Orchin, "Theory and Applications of UV Spectroscopy". One article in particular that derives this result is H. Kuhn, Journal of Chemical Physics, vol 17, p. 1198 (1949) At 02:38 AM 11/1/02, you wrote: >in the literature it is commonly stated that UV absorbtion energies of >polyenes with increasing chain lengths decrease approximately linearly >when plotted against 1/n, the number of repeat units. Does anyone know >where this has been stated for the first time and at which level of theory >this is true exactly. I am writing a paper and I want to give a proper >reference, however, usually people do not give a citation or they just >cite their own previous papers. I suspect that the relationship does not >necessarily hold when higher levels of theory are used and when the >geometries are optimized. Can somebody comment on this? Will Polik From chemistry-request@server.ccl.net Fri Nov 1 10:07:10 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA1F7Af09894 for ; Fri, 1 Nov 2002 10:07:10 -0500 Received: from cornell.edu (dopey.lassp.cornell.edu [128.84.241.121]) by cornell.edu (8.9.3/8.9.3) with ESMTP id KAA21466 for ; Fri, 1 Nov 2002 10:07:09 -0500 (EST) Message-ID: <3DC2989D.70003465@cornell.edu> Date: Fri, 01 Nov 2002 10:07:09 -0500 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Gaussian98W Error with Opt & Freq Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi -- I've optimized and gotten the normal modes of a molecule with charge 0 and multiplicity 1 with Gaussian without a problem. I tried getting the same (OPT & FREQ) with the same molecule but with a charge of 1 and a multiplicity of 2. Unfotunately, the calculation ends in error before completion with the following message: Has anyone gotten this error before and what can be done to get around this? As I said, the neutral molecule case works fine, but the charged one does not... Any ideas would be great. It=199 PL= 6.24D-11 DiagD=TT ESCF= 813.462772 Diff=-3.93D-06 RMSDP= 5.97D-05. It=199 PL= 6.24D-11 DiagD=TT ESCF= 813.462758 Diff=-3.93D-06 RMSDP= 5.97D-05. It=200 PL= 6.24D-11 DiagD=TT ESCF= 813.462795 Diff= 9.27D-07 RMSDP= 5.97D-05. """""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCE DELTAE= 0.2137E-04 DELTAP= 0.6244E-10 Error termination via Lnk1e in C:\G98W\l402.exe. Job cpu time: 0 days 17 hours 23 minutes 36.0 seconds. File lengths (MBytes): RWF= 60 Int= 0 D2E= 0 Chk= 1 Scr= 1 Thanks, Connie From chemistry-request@server.ccl.net Fri Nov 1 13:08:48 2002 Received: from brass.metals.hope.edu ([198.110.98.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gA1I8mf13136 for ; Fri, 1 Nov 2002 13:08:48 -0500 Received: from hope.edu ([198.110.98.17]) by brass.metals.hope.edu (NAVGW 2.5.2.11) with SMTP id M2002110112542910342 ; Fri, 01 Nov 2002 12:54:29 -0500 Received: from [198.110.101.8] (kruegerb@hope.edu) by hope.edu; Fri, 1 Nov 2002 12:54:29 -0500 X-WM-Posted-At: hope.edu; Fri, 1 Nov 02 12:54:29 -0500 Message-Id: <5.1.0.14.0.20021101122600.03079670@mail.hope.edu> X-Sender: kruegerb@mail.hope.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 01 Nov 2002 12:36:38 -0500 To: Ulrike Salzner From: Brent Krueger Subject: Re: CCL:polyene spectra Cc: CHEMISTRY@ccl.net In-Reply-To: <3DC22F78.5060705@fen.bilkent.edu.tr> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Ulrike, This is indeed a complicated problem. The earlier work that Will mentions does verify the energy to 1/n relationship. Note, however, that the transition observed in polyenes is generally S2 <--> S0 and I think that wasn't really understood at the time. I believe real progress in understanding the nature of polyene electronic states (S0, S1, and S2) began in the early 70s. See for instance: Hudson, B. S.; Kohler, B. E. Chem. Phys. Lett. 1972, 14, 299-304. Schulten, K.; Karplus, M. Chem. Phys. Lett. 1972, 15, 305-309. A handy reference that reviews most of this "neo-early" work is: Hudson, B. S.; Kohler, B. E.; Schulten, K. In Excited States; Lim, E. C., Ed.; Academic Press: New York, 1982; Vol. 6, pp 1-95. I must admit that I am not too up on current polyene work, but you should look up recent papers from Hsu and Head-Gordon and from the Robb group. Cheers, Brent At 09:38 AM 11/1/2002 +0200, you wrote: >Hello, >in the literature it is commonly stated that UV absorbtion energies of >polyenes with increasing chain lengths decrease approximately linearly >when plotted against 1/n, the number of repeat units. Does anyone know >where this has been stated for the first time and at which level of theory >this is true exactly. I am writing a paper and I want to give a proper >reference, however, usually people do not give a citation or they just >cite their own previous papers. I suspect that the relationship does not >necessarily hold when higher levels of theory are used and when the >geometries are optimized. Can somebody comment on this? >Thanks in advance, >Ulrike Salzner > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > ____________________________________________ Brent P. Krueger Hope College Phone 616 395 7629 Department of Chemistry FAX 616 395 7118 Peale Science Center Holland, MI 49422-9000 From chemistry-request@server.ccl.net Fri Nov 1 16:54:56 2002 Received: from po4.wam.umd.edu ([128.8.10.166]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA1Lstf19349 for ; Fri, 1 Nov 2002 16:54:56 -0500 Received: from arwen.wam.umd.edu (arwen.umd.edu [129.2.68.73]) by po4.wam.umd.edu (8.9.3/8.9.3) with ESMTP id QAA25416 for ; Fri, 1 Nov 2002 16:54:52 -0500 (EST) Message-Id: <5.1.1.6.0.20021101151346.00abd2c0@imap.wam.umd.edu> X-Sender: oliwalk@imap.wam.umd.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Fri, 01 Nov 2002 16:26:27 -0800 To: chemistry@ccl.net From: olivier walker Subject: Covalent map in Autodock and Autodocktools Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi, To explore the conformation of a dual domain protein, I use Autdock and Autodocktools, making one domain the ligand (I'm just interested in rotating 20 bounds for the 6 residues of the linker) and the other one the macromolecule. I've several questions regarding these two programs: 1) When I create pdbq files from mol2 files (from InsightII), I obtrain completely different files. The file created by Autodock utility program mol2topdbq is fine, but the one created by Autodocktools adds a bunch of ''CONNECT'' word that autodock3 couldn't understand. What did I wrong? Thus, I'm using the command line to create input files to use with autodock3. The most important issue is that I need the extremity of my linker to be stick with the macromolecule. 2) How to create a covalent map with Autodock or Autodocktools? a) With Autodocktools, I tried to select an atom on the macromolecule and then create a covalent map but when I click on the box ''use selection'', I always receive the same message "incorrect ligand file format-unable to write with Z atom". b) How to create such a covalent map with Autogrid and how to specify the 2 atoms I want to be linked? I read the manual or the tutorial for these two programs, but this section is not well documented. I will appreciate any help. Olivier ************************************************** Olivier WALKER Department of Chemistry & Biochemistry University of Maryland College Park, MD 20742 USA ************************************************** Fax : 301-314-0386 Phone : 301-405-8710 E-mail : oliwalk@wam.umd.edu ************************************************** From chemistry-request@server.ccl.net Fri Nov 1 11:02:39 2002 Received: from seupp-smtp.amershambiosciences.com ([192.36.117.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA1G2cf11095 for ; Fri, 1 Nov 2002 11:02:38 -0500 Received: from seupp-ln21.se.apbiotech.com (unverified [193.180.20.124]) by ns.amershambiosciences.com (Rockliffe SMTPRA 5.2.4) with ESMTP id ; Fri, 1 Nov 2002 17:04:02 +0100 Subject: Re: CCL:polyene spectra To: CHEMISTRY@ccl.net Cc: salzner@fen.bilkent.edu.tr X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Message-ID: From: "Najeeb Said" Date: Fri, 1 Nov 2002 16:02:27 +0000 X-MIMETrack: Serialize by Router on seuppln21.xynet.net/Server/xynet(Release 5.07a |May 14, 2001) at 2002-11-01 17:05:53 MIME-Version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gA1G2df11096 Dear Ulrike, The paper below contains the information you are searching for: The Electronic Spectra of Symmetric Cyanine Dyes. A CASPT2 Study Marko Schreiber, Markus P. Fülscher, and Volker Buß, Physical Chemistry - Chemical Physics 2001, 3, 3906-3912. Regards, N Said najeeb.said@uk.amershambiosciences.com "William F. Polik" To: Ulrike Salzner cc: CHEMISTRY@ccl.net, (bcc: Najeeb Said/UK/xynet) Sent by: Subject: CCL:polyene spectra "Computational Chemistry List" 01/11/02 15:04 Ulrike, This is a very common physical chemistry experiment illustrating the Particle-in-a-Box that is described in most physical chemistry laboratory textbooks, as well as in several articles in the Journal of Chemical education over the last decade. You can find several references to the older literature in Chapter 11 of Jaffe & Orchin, "Theory and Applications of UV Spectroscopy". One article in particular that derives this result is H. Kuhn, Journal of Chemical Physics, vol 17, p. 1198 (1949) At 02:38 AM 11/1/02, you wrote: >in the literature it is commonly stated that UV absorbtion energies of >polyenes with increasing chain lengths decrease approximately linearly >when plotted against 1/n, the number of repeat units. Does anyone know >where this has been stated for the first time and at which level of theory >this is true exactly. I am writing a paper and I want to give a proper >reference, however, usually people do not give a citation or they just >cite their own previous papers. I suspect that the relationship does not >necessarily hold when higher levels of theory are used and when the >geometries are optimized. Can somebody comment on this? Will Polik From chemistry-request@server.ccl.net Fri Nov 1 09:29:29 2002 Received: from smtp01.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA1ETRf09217 for ; Fri, 1 Nov 2002 09:29:28 -0500 Received: from PC12 (unknown [202.127.19.236]) by smtp01.sohu.com (Postfix) with ESMTP id DAE2953729; Fri, 1 Nov 2002 22:04:54 +0800 (CST) Date: Fri, 1 Nov 2002 22:31:10 +0800 From: "zgleo" To: Zengjian Hu Cc: "CHEMISTRY@ccl.net" Subject: Re: Re: CCL:Sybyl question X-mailer: Foxmail 4.1 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon425767811408_=====" Message-Id: <20021101140454.DAE2953729@smtp01.sohu.com> This is a multi-part message in MIME format. --=====000_Dragon425767811408_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: quoted-printable Dear Zengjian Hu, =09Thank you for your help.You said I needn't put the ligand into= the active site,did you mean =09the autodock will find the active site or the pocket= automatically?Expecting your reply... Best regards! =A1=A1zgleo =A1=A1zgliu@sohu.com =A1=A12002-11-01 =3D=3D=3D=3D=3D=3D=3D 2002-11-01 14:19:00 zgleo wrote=3D=3D=3D=3D=3D=3D=3D >Hi, > >If you just prepare the ligands for Autodock, you >don't need to put the ligand into the active site >of the receptor. Anywhere is OK. > >Best, > >Hu > >---------------------------------------------- >Zengjian Hu, Ph. D. >Research Investigator >University of Michigan >1150 W. Medical Center Drive >2423 Med. Sci I >Ann Arbor, MI 48109-0934 >Ph# 734-764-2537 >Fax# 734-764-2532 >E-mail: huzengjian@hotmail.com >---------------------------------------------- > > > > > >>From: "zgleo" >>To: "CHEMISTRY@ccl.net" >>Subject: CCL:Sybyl question >>Date: Fri, 1 Nov 2002 15:46:39 +0800 >> >>Dear CCLers, >>=09I find a strange problem when I use sybyl. >>=09I plan to prepare some ligands for autodock. >>=09The first thing I have to do is=09to move these ligands to the= pocket area >>of the receptor. >>=09So I read the receptor molecule and ligand molecule into D1= and >>D2,respectively. >>=09Then I move the ligand to the pocket area by focusing mouse on= D2,and then >>save it as >>=09"ligand.mol2"(Didn't freeze view). >>=09After this,I zap the D2 and read "ligand.mol2" into D2. >>=09It looks that everything is OK----the ligand molecule is= exactly in the >>pocket. >>=09Unfortunately,when I zap everything and read "ligand.mol2"= into sybyl >>firstly and receptor >>=09file into sybyl subsequently,I find the ligand is located far= away from >>the receptor. >>=09Then I change the order again----that is reading the receptor= first and >>the ligand second,to >>=09 my surprise,the ligand is located in the pocket area again. >>=09I'm completely confused by it. >>=09Does anybody know why? >>=09Thanks. >> >> >>Best Regard! >>zgleo >>zgliu@sohu.com >>2002-11-01 >><< fox.gif >> > > >________________________________________________________________= _ >Choose an Internet access plan right for you -- try MSN! >http://resourcecenter.msn.com/access/plans/default.asp =3D =3D =3D =3D =3D =3D =3D =3D =3D =3D =3D =3D =3D =3D =3D =3D =3D =3D =3D =3D =09=09=09 =09 --=====000_Dragon425767811408_===== Content-Type: image/gif; name="fox.GIF" Content-Transfer-Encoding: base64 Content-Disposition: FoxmailIcon; filename="fox.GIF" R0lGODlhIwAfALMLAP///+Dg4OCgAOCAAOAAAMDA4KCgwKBgQIAAAGBggCAgIAAAAAAAAAAAAAAA AAAAACH/C05FVFNDQVBFMi4wAwHoAwAh+QQJDwALACwAAAAAIwAfAAAE+3DJSem5Na+jux3CxWWi 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X70ZtpsVFiC3X74UxcETszKRxxigP0UiCZh2j5Az0BM3XTnexd6pM+MY5k43670BCeYDsqLkY/BO 63QeBCiYRWPDvXizFihA8IESAh73Iq44oKDYQgSyIEYMMRAj0ySHCEKWYXERAYGTJ4H08ravxEKU KK/1otEyA6WbOHPijAAAIfkECQ8ACwAsAgAAACEAHwAABPtwyUnluTWvo7sdwsVlotcdQyIIg+i6 4Gp+haGGQ87m6Fyhg0ChAFwZdQLf5BIMFI3GnkzJDCCh0YFE6xNdm1YBccGlAmPNgqIwUIyUlvOq aWMn3nBmDkRft+E/QAY1QQYKQgqAFC4GAY6PkAqJHQYaBwaDkJoBlRqYJxeZm5+eBaCXmINDNZ2l oEsXCbIJJqpdKJertJSmM0wCokK7FbYmIiEFmsMUjb0esyjJjwXLEqLOGQmY1JeQNdXB2BPaotqr Nd/MmkN7OebUAQntspzLwQFYK+Z1KAIKszaISSuQb86sBQoQgJCEgJejGFj2XFAgKiECWRlUWdmz Qy7igX/bAkiyiKAhMzbtUk4siYCAS5dCqGlb5qWdC4QtX8KcRs0GzRd4RgodSjQCACH+PEZJTEUg SURFTlRJVFkNCkNyZWF0ZWQgb3IgbW9kaWZpZWQgYnkNCkVEIVNPTiAnOTYgW1hmL1VDZl0NCgA7 --=====000_Dragon425767811408_=====-- From chemistry-request@server.ccl.net Fri Nov 1 22:31:00 2002 Received: from ultra.chem.ucsb.edu ([128.111.114.119]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA23Uxf07216 for ; Fri, 1 Nov 2002 22:31:00 -0500 Received: from localhost (bushnell@localhost) by ultra.chem.ucsb.edu (8.12.3/8.12.3) with ESMTP id gA23UusQ019481 for ; Fri, 1 Nov 2002 19:30:56 -0800 (PST) Date: Fri, 1 Nov 2002 19:30:55 -0800 (PST) From: John Bushnell To: chemistry@ccl.net Subject: RE: CCL:Gaussian98W Error with Opt & Freq Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-milter (http://amavis.org/) Some typical things to try: * Increase the maximum number of SCF cycles * Set scf=qc * Do an ROHF calculation first, then guess=read * Look at the guess (using guess=only) and fix it (using guess=alter) * Use a checkpoint file for the neutral, then change the charge and multiplicity and use guess=read * Use a smaller basis set, and increase the size after you have successfully converged the SCF * Using some combination of the above, drag Gaussian kicking and screaming to the desired state Good luck! - John ---------- Forwarded message ---------- Date: Fri, 01 Nov 2002 10:07:09 -0500 From: Connie Chang To: chemistry@ccl.net Subject: CCL:Gaussian98W Error with Opt & Freq Hi -- I've optimized and gotten the normal modes of a molecule with charge 0 and multiplicity 1 with Gaussian without a problem. I tried getting the same (OPT & FREQ) with the same molecule but with a charge of 1 and a multiplicity of 2. Unfotunately, the calculation ends in error before completion with the following message: Has anyone gotten this error before and what can be done to get around this? As I said, the neutral molecule case works fine, but the charged one does not... Any ideas would be great. It=199 PL= 6.24D-11 DiagD=TT ESCF= 813.462772 Diff=-3.93D-06 RMSDP= 5.97D-05. It=199 PL= 6.24D-11 DiagD=TT ESCF= 813.462758 Diff=-3.93D-06 RMSDP= 5.97D-05. It=200 PL= 6.24D-11 DiagD=TT ESCF= 813.462795 Diff= 9.27D-07 RMSDP= 5.97D-05. """""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCE DELTAE= 0.2137E-04 DELTAP= 0.6244E-10 Error termination via Lnk1e in C:\G98W\l402.exe. Job cpu time: 0 days 17 hours 23 minutes 36.0 seconds. File lengths (MBytes): RWF= 60 Int= 0 D2E= 0 Chk= 1 Scr= 1 Thanks, Connie -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Fri Nov 1 22:27:12 2002 Received: from smtp01.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA23RAf07170 for ; Fri, 1 Nov 2002 22:27:11 -0500 Received: from PC12 (unknown [202.127.19.236]) by smtp01.sohu.com (Postfix) with ESMTP id 4AB465366F; Sat, 2 Nov 2002 11:02:37 +0800 (CST) Date: Sat, 2 Nov 2002 11:28:52 +0800 From: "zgleo" To: "DURST_GREGORY@LILLY.COM" Cc: "CHEMISTRY@ccl.net" Subject: Re: Re: CCL:Sybyl question X-mailer: Foxmail 4.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <20021102030237.4AB465366F@smtp01.sohu.com> Dear DURST_GREGORY, Thank you for your help.I have solved the problem by freeze the ligand molecule area.I know the coordinates in host memory will never be changed until the freeze command is used.Any operation is reflected only in the display system.But I have some other questions.You know,when you adjust the location of ligand,you may have to change the visual angle of the macromolecule.Commonly,I chang the mouse focus option to global first and then rotate all the molecules so as to change the visual angle.My question is whether such rotations will change the absolute coordinates of ligand(in display system)?Does the coordinate axis also rotate with the molecule? Best Regards! --------------------- Liu Zhi-Guo Ph.D candidate Drug Design & Discovery Center Shanghai Institute of Materia Medica Shanghai,in China