From chemistry-request@ccl.net Mon Jan 3 12:26:27 2005 Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j03HQP5A016065 for ; Mon, 3 Jan 2005 12:26:26 -0500 Received: by lgdx04.lg.ehu.es id SAA0000027539; Mon, 3 Jan 2005 18:43:05 +0100 (MET) Message-ID: <001d01c4f1bb$aea761c0$4a2ee39e@lcpycx> From: "Pablo Vitoria" To: "Geetha Navada K." , References: Subject: Re: CCL:modredundant and freezing dihedral angles Date: Mon, 3 Jan 2005 18:42:36 +0100 MIME-Version: 1.0 Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2527 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2527 X-Spam-Status: No, hits=1.0 required=7.5 tests=LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Geetha, I recently optimised only the hydrogen atoms in a molecule, and I used the method outlined in pp. 170-171 of the G03 manual. I put all H atoms at the end of the molecule specification (xyz coordinates) to make it easier, and I created cartesian coordinates for all non-H atoms (32) to freeze them (see below). There may be easier ways, but this one works. Pablo ModRedunddant section of the input file: 1 B 2 B 3 B 4 B 5 B 6 B 7 B 8 B 9 B 10 B 11 B 12 B 13 B 14 B 15 B 16 B 17 B 18 B 19 B 20 B 21 B 22 B 23 B 24 B 25 B 26 B 27 B 28 B 29 B 30 B 31 B 32 B * F ----- Original Message ----- From: "Geetha Navada K." To: Sent: Monday, January 03, 2005 9:58 AM Subject: CCL:modredundant and freezing dihedral angles > Hi, > I am trying to use opt=modredundant to selectively optimise (hydrogen > atoms only) in a molecule of 43 atoms. I have the coordinates (xyz) and I > use the wildcard technique to freeze/activate the parameters. > I am able to freeze the intended bond distances and angles, however, all > the dihedral angles are taken as variables, inspite of my input '**** F'. > I donot have access to the interactive interfaces such as Gaussview. > > Any help is greatly appreciated > Thanks > -geetha > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line > and send your message to: CHEMISTRY=at=ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST=at=ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow=at=nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Tue Jan 4 09:34:06 2005 Received: from fgwmail6.fujitsu.co.jp (fgwmail6.fujitsu.co.jp [192.51.44.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j04EY3k9007219 for ; Tue, 4 Jan 2005 09:34:04 -0500 Received: from m6.gw.fujitsu.co.jp ([10.0.50.76]) by fgwmail6.fujitsu.co.jp (8.12.10/Fujitsu Gateway) id j04EovqK006775 for ; Tue, 4 Jan 2005 23:50:57 +0900 (envelope-from m-ito_at_jp.fujitsu.com) Received: from s1.gw.fujitsu.co.jp by m6.gw.fujitsu.co.jp (8.12.10/Fujitsu Domain Master) id j04EovWa016746 for ; Tue, 4 Jan 2005 23:50:57 +0900 (envelope-from m-ito_at_jp.fujitsu.com) Received: from s1.gw.fujitsu.co.jp (s1 [127.0.0.1]) by s1.gw.fujitsu.co.jp (Postfix) with ESMTP id 0ADD437010A for ; Tue, 4 Jan 2005 23:50:57 +0900 (JST) Received: from dm.atsugi.flab.fujitsu.co.jp (dm.atsugi.flab.fujitsu.co.jp [10.36.64.1]) by s1.gw.fujitsu.co.jp (Postfix) with ESMTP id 9C8BA37010D for ; Tue, 4 Jan 2005 23:50:56 +0900 (JST) Received: from dm.atsugi.flab.fujitsu.co.jp by dm.atsugi.flab.fujitsu.co.jp (8.9.3p2/3.7W-041117-Fujitsu Labs. Atsugi Domain Mail Master (NAVGW)) id XAA15030; Tue, 4 Jan 2005 23:50:56 +0900 (JST) Received: from amailserv.atsugi.flab.fujitsu.co.jp ([10.36.100.4]) by dm.atsugi.flab.fujitsu.co.jp (NAVGW 2.5.2.9) with SMTP id M2005010423505526805 ; Tue, 04 Jan 2005 23:50:55 +0900 Received: from localhost (biobio2.cos.flab.fujitsu.co.jp [10.36.127.103]) by amailserv.atsugi.flab.fujitsu.co.jp (8.11.6+Sun/8.11.6) with ESMTP id j04Eos120936; Tue, 4 Jan 2005 23:50:54 +0900 (JST) Date: Tue, 04 Jan 2005 23:48:19 +0900 (JST) Message-Id: <20050104.234819.653215943.Masakatsu Ito_at_atsugi.flab.fujitsu.co.jp> To: chemistry_at_ccl.net Cc: m-ito_at_jp.fujitsu.com Subject: Ionizable residues affect the free energy calc.? From: Masakatsu Ito X-Mailer: Mew version 2.3 on XEmacs 21.1.14 (Cuyahoga Valley) Mime-Version: 1.0 Content-Type: Text/Plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=4.0 required=7.5 tests=INVALID_MSGID,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, I am wondering if an ionizable residue affects the accuracy of free energy calculation. We are trying to calculate the binding free energies of peptides to their receptor molecule using the 'double coupling' method (*) which requires two simulations. The first yields the free energy change, G1, for a transfer of a protonated peptide molecule, PH(+), from water to gas. PH(+)(aq) + Cl(-)(aq) -> PH(+):Cl(-)(gas) One chloride ion is added to neutralize the system. The second yields the free energy change, G2, for decoupling the peptide from the binding site of the solvated receptor, R(-)(aq) . R(-):PH(+)(aq) + Na(+)(aq) + Cl(-)(aq) -> R(-)(aq) + Na(+)(aq) + PH(+):Cl(-)(gas) Here a sodium ion is added to neutralize the system. The binding free energy is then G2 - G1 . But the problem is that the calculation would be more complicated if we consider all the charge configurations of the solvated peptide, PH(+)(aq) and P(aq). Because the protonated residue is arginine so far, I suppose the deprotonated configuration does not have to be considered. But this approximation is bad for lysine or histidine, and how can I estimate the error? Or how can I resolve the problem? I would be very grateful if you give me some advice or point me to articles dealing with similar problems. ( Please tell me if there is any paper estimating the binding affinities of ioniable ligands into a receptor. ) Thanks in advance for any help. Kind Regards, Masakatsu (*) M.K. Gilson et al. Biophys. J. 72, 1047 (1997) ; J. Herman and S, Shankler, Isr. J. Chem. 27,225 (1986) ; L. Zhang and J. Hermans, Proteins: Struct. Func. Gen. 24, 433 (1996); Roux et al. Biophys. J. 71, 670 (1996) -------------------------------------------------------------------- Masakatsu Ito Nanotechnology Research Center FUJITSU LABORATORIES LTD. 10-1 Morinosato-Wakamiya, Atsugi 243-0197 Japan Phone : +81-46-250-8234 Fax : +81-46-250-8844 E-mail m-ito_at_jp.fujitsu.com From chemistry-request@ccl.net Tue Jan 4 12:44:49 2005 Received: from arwen.arqule.com (smtp.arqule.com [64.119.137.200] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with SMTP id j04Hin65017125 for ; Tue, 4 Jan 2005 12:44:49 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: ACS (Comp): Washington DC 2005. Call for Papers Date: Tue, 4 Jan 2005 13:01:40 -0500 Message-ID: <59527B219115AA4CBBE9DEF5D729F222296775$at$ACE.arqule.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: ACS (Comp): Washington DC 2005. Call for Papers Thread-Index: AcTyh3DHwBIhRyjZRbG6dcDDI5H+rg== From: "Smellie, Andrew" To: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j04Hin65017126 230th ACS National Meeting, Washington DC,August 28 - September 1, 2005 COMP division 1st Call for papers The Visualization and Interpretation of Computational Models ============================================================ There are many different approaches available for modeling chemical data. Biological activities can be estimated using a number of approaches such as numerical modeling, pharmacophore construction or structural comparisons. The interaction of small molecules to binding sites can be described using docking models, shape comparisons or pharmacophores. Physico-chemical properties can be estimated using a variety of techniques. All these problems share one common and often unresolved issue. Whatever the model is teaching us about the system in question must be communicated to the clients of the model. This symposium will focus on methods that have been developed to aid in the interpretation of models of all types common in Computational Chemistry. The symposium will not discuss new modeling techniques, but will focus on methods that have been devised to extract the maximum information from the models and communicate that information to clients. Papers are invited that cover issues on * Visualization of Modeling Data * Interpretation of Modeling Data * Communication of knowledge from the model to clients (e.g. chemists, biologists etc) The organizers are Andrew Smellie, Anton Filikov and Rocio Palma of Arqule Inc. Please submit your abstracts to asmellie$at$arqule.com no later than April 2nd 2005 Dr. Andrew Smellie Senior Scientist Arqule Inc. 19 Presidential Way, Woburn MA 01801 USA asmellie$at$arqule.com 781-994-0559 (direct) 781-994-0679 (fax) From chemistry-request@ccl.net Tue Jan 4 09:32:26 2005 Received: from cliff.niehs.nih.gov (cliff.niehs.nih.gov [157.98.192.45]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j04EWPk9007123 for ; Tue, 4 Jan 2005 09:32:25 -0500 Received: from cliff.niehs.nih.gov (localhost.localdomain [127.0.0.1]) by cliff.niehs.nih.gov (8.12.11/8.12.11/tx-1.16) with ESMTP id j04EnIIa022066 for ; Tue, 4 Jan 2005 09:49:18 -0500 Received: from [157.98.73.159] (ip073159.niehs.nih.gov [157.98.73.159]) by cliff.niehs.nih.gov (8.12.11/8.12.11/rx-1.12) with ESMTP id j04EnIIh022061 for ; Tue, 4 Jan 2005 09:49:18 -0500 Subject: Problems with ESP from g98 rev. A9 From: "G. Andres Cisneros" To: chemistry)at(server.ccl.net Content-Type: text/plain Organization: NIH Message-Id: <1104850158.8750.22.camel@bagan> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.6 (1.4.6-2) Date: Tue, 04 Jan 2005 09:49:18 -0500 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, I'm trying to compare electrostatic potential (ESP) for water at different points calculated from a cube file and with non-standard input with g98. However I've noticed that the maximum value for ESP for the same geometry does not agree!. My input geometry looks like this: 8 0.00000000 0.00000000 0.00000000 1 0.67956100 0.87766500 0.00000000 1 0.67956100 -0.87766500 0.00000000 If I calculate the ESP in a medium cube, the maximum value is 136.656 at (0.015492,0.015492,0.015492). However, if I use a non-standard input and specify that same point I get a value of 136.597912. The nonstd input looks like this: #P nonstd 1/38=1/1; 2/15=1,17=6,18=5/2; 3/5=1,6=6,7=1,8=2,11=2,25=1,30=1/1,2,3; 4//1; 5/5=2,32=1,38=4,42=-5/2; 6/7=3,15=1,28=1,/1,2; 99/5=1,9=1/99; In both cases I'm using b3lyp/6-31G* with no symmetry for the calculations. Has anyone seen something like this before?, Which value should I trust?, (I'm leaning towards the second one but I'm not sure). Thanks in advance, Andres -- G. Andres Cisneros, Ph.D. NIEHS, 111 T.W. Alexander Dr. MD F0-08, PO Box 12233 RTP, NC 27707 tel (919) 541 4663 fax (919) 541 0779