From chemistry-request@ccl.net Tue Mar 30 05:40:34 2004 Received: from guppy.vub.ac.be (www.vub.ac.be [134.184.129.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2UAeWjs014258 for ; Tue, 30 Mar 2004 05:40:32 -0500 Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.8]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.1.ap (guppy)) id MAA16071; Tue, 30 Mar 2004 12:43:45 +0200 (MET DST) for Received: from ulb.ac.be (chimorg-pc5.ulb.ac.be [164.15.61.104]) by mach.vub.ac.be (Postfix) with ESMTP id 403BC27E5 for ; Tue, 30 Mar 2004 12:43:40 +0200 (CEST) Message-ID: <4069CA7A.5040807(at)ulb.ac.be> Date: Tue, 30 Mar 2004 21:28:58 +0200 From: Christophe Biot Organization: ULB User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: fr, en-us MIME-Version: 1.0 To: Liste CCL Subject: non additivity X-Priority: 1 (highest) Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.3 required=7.0 tests=DATE_IN_FUTURE_06_12, PRIORITY_NO_NAME,X_PRIORITY_HIGH autolearn=no version=2.61 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, It's well known that description of dispersion interactions responsible (for example) for the stabilization of the stacked nucleic acid bases in DNA requires inclusion of the effects of correlation. I am just asking myself how dispersion is taken into account when calculating the total interaction energy into many-body interaction contributions? For example, at HF or MP2 level. Is there a difference when performing CCSD(T) calculations? Best wishes, Christophe Biot From chemistry-request@ccl.net Tue Mar 30 02:57:39 2004 Received: from antivirus.unimo.it (antivirus.unimo.it [155.185.1.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2U7vcjs004800 for ; Tue, 30 Mar 2004 02:57:39 -0500 Received: from far70.unimore.it (far70.unimo.it [155.185.29.70]) by antivirus.unimo.it (8.12.11/8.12.11) with ESMTP id i2U80ow8025482 for ; Tue, 30 Mar 2004 10:00:50 +0200 Message-Id: <6.0.3.0.0.20040330095912.01b42988-.at.-mail.unimo.it> X-Sender: ferranna-.at.-mail.unimo.it X-Mailer: QUALCOMM Windows Eudora Version 6.0.3.0 Date: Tue, 30 Mar 2004 10:00:52 +0200 To: chemistry-.at.-ccl.net From: Anna Ferrari Subject: Makefile for DOCK5.1.1 on IBM-AIX Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Virus-Scanned: by amavisd-milter on antivirus (http://amavis.org/) X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, is there available a Makefile to compile DOCK 5.1.1 and GRID on a multiprocessor IBM-AIX computer? Thank you very much in advance Regards, Anna From chemistry-request@ccl.net Tue Mar 30 09:47:06 2004 Received: from polaris.scs.uiuc.edu (polaris.scs.uiuc.edu [130.126.231.226]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2UEl5js028032 for ; Tue, 30 Mar 2004 09:47:05 -0500 Received: from leonidas (leonidas.scs.uiuc.edu [130.126.226.239]) by polaris.scs.uiuc.edu (8.12.10/8.12.10) with SMTP id i2UEoKxg21729557 for ; Tue, 30 Mar 2004 08:50:20 -0600 (CST) Reply-To: From: "Jerome Baudry" To: Subject: suggestions for secondary structure -> protein structure prediction ? Date: Tue, 30 Mar 2004 08:48:31 -0600 Message-ID: <002c01c41666$128ecc00$efe27e82@leonidas> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All I have NMR information about the secondary structure(s) of several domains of a protein. Is there a relatively fast way to propose (and rank) different folding solutions for the complete protein, from the domains assigned with secondary structures? I was thinking maybe about an homology-modeling-like approach where PMF of several possible associations for these secondary elements would be calculated, or a scoring function, or maybe a full potential energy function, where the assembly of the secondary elements rigid-body blocks would be automated and somehow combinatorialized.... I am not looking at a folding pathway/trajectory, but at somehow ranking different final solutions. Any suggestions of possible approaches/literature/software ? Thanks a lot in advance... ---------------------------------------------------------- Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager. School of Chemical Sciences University of Illinois at Urbana-Champaign 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120; e-mail: jerome-.at.-scs.uiuc.edu From chemistry-request@ccl.net Tue Mar 30 04:20:36 2004 Received: from yangtze.hku.hk (yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2U9KYjs009084 for ; Tue, 30 Mar 2004 04:20:35 -0500 Received: from yangtze.hku.hk (yangtze.hku.hk [127.0.0.1]) by yangtze.hku.hk (8.12.8/8.12.8) with ESMTP id i2U9H5uT024066 for ; Tue, 30 Mar 2004 17:17:05 +0800 Received: from localhost (xzheng@localhost) by yangtze.hku.hk (8.12.8/8.12.8/Submit) with ESMTP id i2U9Gtr9024060 for ; Tue, 30 Mar 2004 17:17:05 +0800 Date: Tue, 30 Mar 2004 17:16:55 +0800 (HKT) From: xzheng-.at.-yangtze.hku.hk To: chemistry-.at.-ccl.net Subject: ADT problem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.3 required=7.0 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All, I'm using AUTODOCK tools. But I'm now facing a problem which is : The tools cannot produce any *.PDBQS file. Why is that? Thank you in advance. ZX From chemistry-request@ccl.net Tue Mar 30 02:13:55 2004 Received: from rzcomm7.rz.tu-bs.de (rzcomm7.rz.tu-bs.de [134.169.9.53]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2U7Drjs003092 for ; Tue, 30 Mar 2004 02:13:54 -0500 Received: from localhost (localhost [127.0.0.1]) by rzcomm7.rz.tu-bs.de (8.11.1/8.11.1) with ESMTP id i2U7H1i15603 for ; Tue, 30 Mar 2004 09:17:01 +0200 (METDST) Received: from rzcomm7.rz.tu-bs.de ([127.0.0.1]) by localhost (rzcomm7 [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 15246-02 for ; Tue, 30 Mar 2004 09:17:01 +0200 (METDST) Received: from rzcomm12.rz.tu-bs.de (rzcomm12.rz.tu-bs.de [134.169.9.59]) by rzcomm7.rz.tu-bs.de (8.11.1/8.11.1) with ESMTP id i2U7FJ615352 for ; Tue, 30 Mar 2004 09:15:23 +0200 (METDST) Received: from tu-bs.de (pc1.org-chem.nat.tu-bs.de [134.169.44.154]) by rzcomm12.rz.tu-bs.de (8.11.1/8.11.1) with ESMTP id i2U7FI826649 for ; Tue, 30 Mar 2004 09:15:19 +0200 (METDST) Message-ID: <40691E0E.7050003~at~tu-bs.de> Date: Tue, 30 Mar 2004 09:13:18 +0200 From: Joerg Grunenberg User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; de-DE; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: de-de, de MIME-Version: 1.0 To: CHEMISTRY~at~ccl.net Subject: Re: CCL:force constant and zmatrix References: <40689E0C.4010103~at~ilion.bio.sunysb.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new at tu-bs.de X-Spam-Status: No, hits=0.0 required=7.0 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 Hello Guanglei, the literature is full of coordinate-dependent force constants. Since force constants are the energy second derivatives they are arranged in a matrix containing both, non-zero diagonal and non-zero off-diagonal elements. Changing the coordinate system means changing the coupling constants. There are two ways to solve the problem: 1) diagonalize your force constant matrix. You will get unique force constants but they will describe delocalized displacements... or 2) build the inverse of your force constant matrix. You will get unique force constants in a compliance matrix. See for example: J. Grunenberg, N. Goldberg, J. Am. Chem. Soc. 2000, 12, 6045 J. Grunenberg, R. Streubel, G. v. Frantzius and W. Marten J. Chem. Phys. 2003, 119 Greetings, Joerg Guanglei Cui schrieb: > Hi, > > I tried some frequency calculation with Gaussian03 to obtain the force > constants of certain internal degree of freedom. However, the results > depended greatly on how the input z-matrix is defined. My question is > why this projection is z-matrix-definition dependent, and what is the > best way to do such calculations. Thanks in advance. > > Guanglei > -- Jvrg Grunenberg, Org. Chemie, Hagenring 30, 38106 Braunschweig email: Joerg.Grunenberg~at~tu-bs.de phone: +49 531 391 5252 URL: http://www.oc.tu-bs.de/Grunenberg From chemistry-request@ccl.net Tue Mar 30 07:39:23 2004 Received: from dfu07.dfh.dk (dfu07.dfh.dk [130.225.252.202]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2UCdKjs021291 for ; Tue, 30 Mar 2004 07:39:21 -0500 Received: from dfu08.dfh.dk (dfu08.dfh.dk [130.225.252.203]) by dfu07.dfh.dk (8.11.6/8.11.6) with ESMTP id i2UDimS18396 for ; Tue, 30 Mar 2004 13:44:48 GMT Received: from dhcp225-96.dfh.dk ([130.225.225.96]) by dfu08.dfh.dk (MailMonitor for SMTP v1.2.2 ) ; Tue, 30 Mar 2004 14:44:36 +0200 (CEST) From: "Lars Olsen" To: Subject: Crystal packing energy Date: Tue, 30 Mar 2004 14:40:17 +0200 Message-ID: <001901c41654$284ff850$60e1e182@mlob> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001A_01C41664.EBD8C850" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4510 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal X-Spam-Status: No, hits=0.2 required=7.0 tests=HTML_70_80, HTML_FONTCOLOR_UNKNOWN,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_001A_01C41664.EBD8C850 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, =20 We would like to determine crystal packing energies of 3D crystalline structures of polar =20 (and salts of) organic compounds (up to 20 heavy atoms). Therefore, we = are interested in=20 programs that are available for that purpose. In addition, references to previous work of the=20 same kind would also be very interesting to us.=20 =20 Best regards,=20 Lars=20 ---------------------------------------------------------------- Lars Olsen Danish University of Pharmaceutical Sciences Universitetsparken 2 DK- 2100 Copenhagen =D8 Denmark E-mail: Lo~at~dfuni.dk Phone: +45 35 306 305 =20 =20 ------=_NextPart_000_001A_01C41664.EBD8C850 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear CCLers,

 

We would like to determine crystal packing energies = of 3D crystalline structures of polar =A0

(and salts of) organic compounds = (up to 20 heavy atoms). Therefore, we are interested in

programs that are available for = that purpose. In addition, references to previous work of the =

same kind would also be very = interesting to us.

 

Best regards,

Lars

------------------------------------------------------= ----------

Lars Olsen

Danish University of Pharmaceutical Sciences

Universitetsparken 2

DK- 2100 Copenhagen =D8

Denmark

E-mail: Lo~at~dfuni.dk

Phone: +45 35 306 305

 

 

------=_NextPart_000_001A_01C41664.EBD8C850-- From chemistry-request@ccl.net Tue Mar 30 13:49:50 2004 Received: from postfix3-1.free.fr (postfix3-1.free.fr [213.228.0.44]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2UInojs009953 for ; Tue, 30 Mar 2004 13:49:50 -0500 Received: from [82.65.4.120] (lns-vlq-1-82-65-4-120.adsl.proxad.net [82.65.4.120]) by postfix3-1.free.fr (Postfix) with ESMTP id 990E0C4318; Tue, 30 Mar 2004 20:53:01 +0200 (CEST) In-Reply-To: <40689E0C.4010103!at!ilion.bio.sunysb.edu> References: <40689E0C.4010103!at!ilion.bio.sunysb.edu> Mime-Version: 1.0 (Apple Message framework v613) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: Content-Transfer-Encoding: 7bit Cc: chemistry!at!ccl.net From: hinsen!at!cnrs-orleans.fr Subject: Re: CCL:force constant and zmatrix Date: Tue, 30 Mar 2004 08:59:40 +0200 To: Guanglei Cui X-Mailer: Apple Mail (2.613) X-Spam-Status: No, hits=3.5 required=7.0 tests=DATE_IN_PAST_06_12, NO_REAL_NAME,RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On 30.03.2004, at 00:07, Guanglei Cui wrote: > I tried some frequency calculation with Gaussian03 to obtain the force > constants of certain internal degree of freedom. However, the results > depended greatly on how the input z-matrix is defined. My question is > why this projection is z-matrix-definition dependent, and what is the > best way to do such calculations. Thanks in advance. > Force constants are partial derivatives, their full specification includes the full set of coordinates of the system, i.e. also those that are kept fixed. To take a simple (and unrealistic) example, consider a quadrilateral arrangement of bonded atoms * ---a---* | | b d | | *---c---* The force constant for a obviously depends on what you keep fixed: if you keep the angles fixed, then c will change along with a, if you keep the other distances fixed, then all the angles will change. -- ------------------------------------------------------------------------ ------- Konrad Hinsen | E-Mail: hinsen!at!cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------ ------- From chemistry-request@ccl.net Tue Mar 30 13:22:51 2004 Received: from smtp4.es.uci.edu (smtp4.es.uci.edu [128.200.80.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2UIMojs008536 for ; Tue, 30 Mar 2004 13:22:50 -0500 Received: from qiang (vp087184.reshsg.uci.edu [128.195.87.184]) by smtp4.es.uci.edu (8.12.8/8.12.8) with ESMTP id i2UIPsHZ002555 for ; Tue, 30 Mar 2004 10:25:56 -0800 Message-Id: <200403301825.i2UIPsHZ002555(at)smtp4.es.uci.edu> Date: Tue, 30 Mar 2004 10:25:37 -0800 From: "Qiang Lu" Reply-To: qiangl(at)uci.edu To: "chemistry" Subject: Re: CCL:force constant and zmatrix X-mailer: Foxmail 5.0 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=1.1 required=7.0 tests=MIME_BASE64_TEXT autolearn=no version=2.61 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id i2UIMpjs008550 Dear all, I wander is it ok to use the force constant directly come from QM calculation. I heard of that it is not good to use QM force constant directly into MM calculations. Does anyone know about this? Qiang Lu ======= 2004-03-29 23:13:18 DzTZ@4PEVPP45@#:======= >Hello Guanglei, > > >the literature is full of coordinate-dependent force constants. > >Since force constants are the energy second derivatives they are >arranged in a matrix containing both, non-zero diagonal and non-zero >off-diagonal elements. Changing the coordinate system means changing the >coupling constants. There are two ways to solve the problem: > >1) diagonalize your force constant matrix. You will get unique force >constants but they will describe delocalized displacements... >or >2) build the inverse of your force constant matrix. You will get unique >force constants in a compliance matrix. > >See for example: > >J. Grunenberg, N. Goldberg, J. Am. Chem. Soc. 2000, 12, 6045 >J. Grunenberg, R. Streubel, G. v. Frantzius and W. Marten J. Chem. >Phys. 2003, 119 > > >Greetings, > >Joerg > > > >Guanglei Cui schrieb: > >> Hi, >> >> I tried some frequency calculation with Gaussian03 to obtain the force >> constants of certain internal degree of freedom. However, the results >> depended greatly on how the input z-matrix is defined. My question is >> why this projection is z-matrix-definition dependent, and what is the >> best way to do such calculations. Thanks in advance. >> >> Guanglei >> >-- >Jvrg Grunenberg, Org. Chemie, Hagenring 30, 38106 Braunschweig >email: Joerg.Grunenberg(at)tu-bs.de phone: +49 531 391 5252 >URL: http://www.oc.tu-bs.de/Grunenberg > > > > > >-= 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) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > = = = = = = = = = = = = = = = = = = = = !!!!!!!!!!!!!!!!VB @q#! !!!!!!!!!!!!!!!!Qiang Lu !!!!!!!!!!!!!!!!qiangl(at)uci.edu !!!!!!!!!!!!!!!!!!!!2004-03-30 From chemistry-request@ccl.net Tue Mar 30 12:41:42 2004 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2UHffjs006535 for ; Tue, 30 Mar 2004 12:41:42 -0500 Received: from smeagol.unb.ca (smeagol.unb.ca [131.202.3.52]) by mailserv.unb.ca (8.12.10/8.12.10) with ESMTP id i2UHeV3v021280; Tue, 30 Mar 2004 13:40:31 -0400 Received: from smeagol.unb.ca (localhost.localdomain [127.0.0.1]) by smeagol.unb.ca (8.12.8/8.12.8) with ESMTP id i2UHihiW024151; Tue, 30 Mar 2004 13:44:43 -0400 Received: (from apache@localhost) by smeagol.unb.ca (8.12.8/8.12.8/Submit) id i2UHicYQ024097; Tue, 30 Mar 2004 13:44:38 -0400 Received: from athlon2.chem.unb.ca (athlon2.chem.unb.ca [131.202.171.176]) by webmail.unb.ca (IMP) with HTTP for ; Tue, 30 Mar 2004 13:44:38 -0400 Message-ID: <1080668678.4069b20608f56-.at.-webmail.unb.ca> Date: Tue, 30 Mar 2004 13:44:38 -0400 From: Joey Harriman To: xzheng-.at.-yangtze.hku.hk Cc: chemistry-.at.-ccl.net Subject: Re: CCL:ADT problem References: In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.171.176 X-UNB-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: X-MailScanner-From: s808o-.at.-unb.ca X-Spam-Status: No, hits=0.0 required=7.0 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 Hi, Are you sure that ADT is not producing the *.pdbqs file. If you are running ADT in windows it sometimes places the receptor files in the scratch folder. You can check this by running a quick search of your hard drive to see if the file is fould elsewhere. Additionally, what are you using as an input for the pdbqs? If it is a mol2 file there may be a problem with how the file is parsed if it was saved in linux and brought into windows (or vice versa). Hope this might help. Cheers, Joey Quoting xzheng-.at.-yangtze.hku.hk: > > Dear All, > > I'm using AUTODOCK tools. But I'm now facing a problem which is : > > The tools cannot produce any *.PDBQS file. Why is that? > > Thank you in advance. > > ZX > > > > -= 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > ---------------------------------- Joey Harriman MSc Computational Chemistry University of New Brunswick Room 228 Toole Hall s808o-.at.-unb.ca 476-6543 ---------------------------------- From chemistry-request@ccl.net Tue Mar 30 16:57:21 2004 Received: from sentry.ucr.edu (sentry.ucr.edu [138.23.226.224]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2ULvKjs018564 for ; Tue, 30 Mar 2004 16:57:20 -0500 Received: from dopetec (dunn4470.ucr.edu [138.23.156.82]) by sentry.ucr.edu (Mirapoint Messaging Server MOS 3.3.8-GR) with ESMTP id AWS72043 for ; Tue, 30 Mar 2004 14:00:35 -0800 (PST) Reply-To: From: "Donald Keidel" To: Subject: CCL: Summary of program to determine structurally important water molecules Date: Tue, 30 Mar 2004 14:00:15 -0800 Organization: UCR Message-ID: <000001c416a2$6471a920$529c178a@dopetec> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4510 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=0.0 required=7.0 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i2ULvLjs018570 I have summarized the responses I have received regarding finding a program that can determine structurally important water molecules in crystal structures. Here are the responses I received. Thank you to all that have responded....all responses have been very helpful. Have a good day. Don Dear Donald, this is not a silly question. Some time ago a collegue of mine posted a question same to yours, and discussion continued for weeks. The right answer doesn't exist. At my experience, the best program to manage water positions (especially > from pdb by xray structures) is GRID. (http://www.moldiscovery.com) It is really powerful and includes a special keyword LEAU to analyze about water position. In the most straightforward way you could evaluate your structure using a water probe, and you can keep only water molecules that make strongest interactions. Wonderful is that GRID it's free for academics. (if I well remember) Hope this can help you, my best whishes, Stefano Dear Don I fitted some functions that can distinguish between these two types of water molecules, on the one hand structural or tightly-bound and on the other losely bound or not that important (or reliable) from the pdb structure of the protein. They are easy to use (or code up) and employ the B factors of water molecules, their solvent accessible contact surface area, and number of protein contacts within 3.5 Angstroms (optionally, also the water molecule hydrogen bond energy as determined by WHAT IF). You can see get the coefficients from the paper: J. Mol. Model. 2003, Vol. 9, issue 3, pages 172-182 or through my webpage. Hope this helps and good luck Alfonso Hi Don, There's a program that I've used to locate water molecules that are in sites of good iteraction energy. The program is called "MMC" and is available > from Dr. Mezei at Mt Sinai School of Medicine http://inka.mssm.edu/docs/molmod/mmc.html The 'Structurally important' aspect will have to come from somewhere else.. But at least you would be able to say that there is a water here based on energetic considerations. It allows you to both conduct a Grand Canonical Ensemble simulation where by lowering the chemical potential, you can find conserved water, Resat H, Mezei M. Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate. Biophys J. 1996 Sep;71(3):1179-90. PMID: 8873992 Or, you if you have the results of an explicit solvent simulation (either MC or MD), you can analyse them to find 'Generic Sites'. The program will report these, and their %occupancy throughout the trajectory. Best Wishes, Josh Hi Don, I've got a simple program called pdbdist, which reads a PDB file, and finds the closest atoms/molecules from a given reference atom. It works under UNIX, and all you have to do is compile it. With the program, you may find waters within the active site or so. Whether or not there are (other) water molecules that are structurally important, is another question. However, you should realize that when there are crystal waters present in a PDB file, they are already well defined, e.g. structurally important; said otherwise, if a water molecule moves around all the time, it is not well defined enough to be characterized by X-ray crystallography, and probably is less important. Donald, GRID can do that, it is available for UNIX,it is free. Gabriele Cruciani checkout out dowser by Jan Hermans (UNC chapel hill). David. ---------------------------------------------------------------------------- ----------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dopetec-.at.-dslextreme.com webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm