From chemistry-request@server.ccl.net Fri Dec 6 01:51:13 2002 Received: from moon ([195.170.158.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB66pCA24583 for ; Fri, 6 Dec 2002 01:51:13 -0500 Received: (from localhost user: 'markku', uid#1889) by hybrid.fi with ESMTP id ; Fri, 6 Dec 2002 08:51:05 +0200 Date: Fri, 6 Dec 2002 08:51:05 +0200 (EET) Sender: Markku Laukkanen From: Markku Laukkanen X-Sender: markku@hybrid.fi cc: chemistry@ccl.net Subject: Re: CCL:Peptides Database In-Reply-To: <003101c29c81$88fad790$91a54084@NottingHill> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To: unlisted-recipients:; (no To-header on input) Hi all too! On Thu, 5 Dec 2002, Andrea Scaiewicz wrote: > hi to all, > > > I am interested in biologically active peptides. Do you know any relevant database? > thanks in advance I am also interested in the same kind of database, mainly molecules where some of the descriptors (100-200) are calculated and the real actual activity/Soluability/permiability is maybe measured in the laboratory. Would be very interested from any links. Thx, PKY > > > Andrea Scaiewicz > > From chemistry-request@server.ccl.net Fri Dec 6 07:56:39 2002 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB6CucA15059 for ; Fri, 6 Dec 2002 07:56:38 -0500 Received: from as2100.itodys.jussieu.fr (as2100.itodys.jussieu.fr [134.157.24.23]) by shiva.jussieu.fr (8.12.5/jtpda-5.4) with SMTP id gB6CubjC061231 for ; Fri, 6 Dec 2002 13:56:37 +0100 (CET) Date: Fri, 6 Dec 2002 13:56:36 +0100 Message-Id: <02120613563688@itodys.jussieu.fr> From: petitjean@itodys.jussieu.fr To: CHEMISTRY@ccl.net Subject: CCL:file formats/mol. medels; was:V3000 molfile format X-VMS-To: SMTP%"CHEMISTRY@ccl.net" X-Antivirus: scanned by sophie at shiva.jussieu.fr To: CHEMISTRY@ccl.net Subj: CCL:file formats/mol. medels; was:V3000 molfile format A public discussion in this list should be nice, and standards may emerge from it. I do not believe that an universal format is possible (too many situations), and the molecular models should be defined before specifying any practical format. Being a user, the first requirement that I propose is to define one or several parameters specifying which kind of information follows (including a release parameter). Then, a set a models should be defined: chemical graph only, 3D only, chemical graph plus one or more 3D, and so on... A list of widely accepted bond types should be welcome. Some other problems: unknown atoms or bond types, free sites for connectivity, Markush (i.e. generic) formulas for reactions or patents, superatoms, polymers (how many units), alloys, coefficients for components, and so on (there are indeed much more complicated situations). It is clear for me that specialists of chemical data banks are able to do many useful suggestions in this area. Computational chemistry and modeling applications have their own requirements, and there are many others. But nothing will end before beginning. Last remark: any programmer should be able read and write molecular formats (think also to read backward in large databases), without having to pay amounts of euros or dollars to get black box routines provided by companies (think to the catastrophic situation on Windows PC). Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean@ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html >If anyone would like to engage in a more detailed discussion about this >issue or anything else connected with chemical structure representation >please contact me directly at k.taylor@mdl.com. From chemistry-request@server.ccl.net Fri Dec 6 12:00:24 2002 Received: from compchem.dfh.dk ([130.225.225.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB6H0OA21243 for ; Fri, 6 Dec 2002 12:00:24 -0500 Received: (from jeremy@localhost) by compchem.dfh.dk (SGI-8.9.3/8.9.3) id RAA77357 for chemistry@ccl.net; Fri, 6 Dec 2002 17:49:15 +0100 (MET) Date: Fri, 6 Dec 2002 17:49:15 +0100 From: "Jeremy R. Greenwood" To: chemistry@ccl.net Subject: Two visualisation questions Message-ID: <20021206174915.C1154947@compchem.dfh.dk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i Dear CClist, Two questions regarding visualisation of data, before I immerse myself in rendering or maths toolkits unnecessarily: ---------------------------------------------------------------------- 1) I have data sets of molecular fields of the form (Xn,Yn,Xn,Pn) (property calculated by QM at various descrete cartesian co-ordinates) that I'd like to visualise, preferably in 3D/stereo with at the very least colour coding of points. 3D interpolation and isocontour surfaces would be a bonus. I have tools (Golpe, InsightII) for handling formatted chemical data so long as it is grid-based. Problem is that I'd rather not work on a rectangular grid -- the points are expensive to calculate, and not many small molecules have a cubic skeleton. So I'd like a general solution for arbitrary points P(X,Y,Z), in any order. It need not necessarily be chemistry-related to software; could be sourced from any discipline that needs this sort of 3D(4D) visualisation, though being able to visualise a molecule simultaneously would be nice. n (number of points) is only going to be in the 100s-1000s. ---------------------------------------------------------------------- 2) (much easier) Can someone recommend me a favourite tool for converting QM spectral intensity data (IR,VCD,UV,nmr,etc.) from e.g. Gaussian (+ reformatting if necessary) into something that looks convincingly like a spectrum to a spectroscopist, using e.g. Lorentzian curves? ---------------------------------------------------------------------- Platform preference: IRIX would be ideal for the 3D, and a windows.exe solution for either would be last resort only. Thanks in advance, Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy@greenwood.net Department of Medicinal Chemistry bh +45 35306117 Royal Danish School of Pharmacy fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Dec 6 06:17:31 2002 Received: from aspirine.u-strasbg.fr ([130.79.84.250]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB6BHVA13236 for ; Fri, 6 Dec 2002 06:17:31 -0500 Received: from hit8.pharma.u-strasbg.fr (lead2.u-strasbg.fr [130.79.85.21]) (authenticated) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id gB6BBPt21645 for ; Fri, 6 Dec 2002 12:11:26 +0100 Message-Id: <5.1.0.14.0.20021206121354.01c08008@aspirine.u-strasbg.fr> X-Sender: rognan@aspirine.u-strasbg.fr X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 06 Dec 2002 12:15:28 +0100 To: chemistry@ccl.net From: Didier Rognan Subject: DOCK5 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCLers, Does anyone know how to save several poses (e.g. 30) when docking a single ligand using DOCK5 ? Thanks for you answers ? ----------------------------------------------------------------------------------------------- Dr. Didier ROGNAN Directeur de Recherches - CNRS Laboratoire de Pharmacochimie de la Communication Cellulaire UMR 7081 74, route du Rhin, B.P.24 F-67401 Illkirch phone: +33 (0)3 90 24 42 35 fax: +33 (0)3 90 24 43 10 mobile: +33 (0)6 89 56 24 46 email: didier.rognan@pharma.u-strasbg.fr From chemistry-request@server.ccl.net Fri Dec 6 00:21:34 2002 Received: from cascara.uvic.ca ([142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB65LYA23290 for ; Fri, 6 Dec 2002 00:21:34 -0500 Received: from [24.65.168.211] ([24.65.168.211]) by cascara.uvic.ca (8.12.6/8.12.6) with ESMTP id gB65KVJ8267472; Thu, 5 Dec 2002 21:21:27 -0800 From: Roy Jensen To: james.metz@abbott.com Cc: chemistry@ccl.net Subject: Re: CCL:constrained multiple linear regression Date: Thu, 05 Dec 2002 21:21:58 -0800 Message-ID: References: In-Reply-To: X-Mailer: Forte Agent 1.91/32.564 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-UVic-Virus-Scanned: OK - Passed virus scan by Sophos (sophie) on cascara X-Scanned-By: MIMEDefang 2.19 (www . roaringpenguin . com / mimedefang) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gB65LYA23291 Excel does multiple linear regression with the LINEST function (from the Insert:Function menu). It isn't obvious that it will work from the description. I can fax you (and everyone else who is interested) the pages from our lab-manual that explains the procedure. In reading your request, I noticed that you need to impose constraints. To apply constraints, use the Solver add-in. NOTE: LINEST is a linear regression method (analytical solution) whereas Solver is a non-linear algorithm (numeric). Solver can, and does, converge to local minima. Roy Jensen -----BEGIN PGP PUBLIC KEY BLOCK----- Comment: available at www.consol.ca ------END PGP PUBLIC KEY BLOCK------ On Mon, 2 Dec 2002 19:08:14 -0600, you wrote: > CCL, > > I am looking for software (preferably free or inexpensive, code is > OK) that will allow me to perform > constrained multiple linear regression. For example, I have an equation > of the form: > > Y = a*X1 + b*X2 + c*X3 + d > > where: Y is the dependent variable > X1 - X3 are independent variables (more than 1) > a, b, c are coefficients > d is a constant > > I must be able to constrain the range of values for a, b, c, and d > during the fitting. > > Please note that programs such as JMP, KalediaGraph, GraphPad > Prism, and several other packages do > NOT allow the user to do this, especially for more than one independent > variable. > > Can someone suggest a program or code to do this? > > Thank you, > Jim Metz > > > James T. Metz, Ph.D. > Research Investigator Chemist > > GPRD R46Y AP10-2 > Abbott Laboratories > 100 Abbott Park Road > Abbott Park, IL 60064-6100 > U.S.A. > > Office (847) 936 - 0441 > FAX (847) 935 - 0548 > > james.metz@abbott.com From chemistry-request@server.ccl.net Fri Dec 6 03:27:24 2002 Received: from pallas_ex003.pallas_uk ([195.167.133.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB68ROA27991 for ; Fri, 6 Dec 2002 03:27:24 -0500 Received: by pallas_ex003.pallas_uk with Internet Mail Service (5.5.2653.19) id ; Fri, 6 Dec 2002 08:30:50 -0000 Message-ID: <2A5044E3B5F36440814C888668E9D6A564EA9E@pallas_ex003.pallas_uk> From: David Clark To: "'chemistry@ccl.net'" Subject: HTS Data Analysis Tools: Summary Date: Fri, 6 Dec 2002 08:30:40 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) 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 gB68ROA27998 Hi all I promised a summary of responses to my query: "Does anyone have any experience that they would be willing to share of tools for HTS data analysis, particularly those that aim to help in the analysis of (qualitative) SAR?". Thanks to all who responded. David Clark **************************************************************************** *********************************** SUMMARY **************************************************************************** *********************************** Dear David, We used the ClassPharmer suite of programs (http://www.bioreason.com) for analysing HTS or virtual screening data. It presents the advantage to cluster compounds by chemical scaffolds which are calculated on the fly. On the defined classes, you can perform various statistical analyses (e.g. scaffold enrichment, score distribution) for detecting false positives. The software can be downloaded from the Bioreason web site and used for a short evaluation. Best regards ---------------------------------------------------------------------------- ------------------- Dr. Didier ROGNAN Directeur de Recherches - CNRS Laboratoire de Pharmacochimie de la Communication Cellulaire UMR 7081 74, route du Rhin, B.P.24 F-67401 Illkirch phone: +33 (0)3 90 24 42 35 fax: +33 (0)3 90 24 43 10 mobile: +33 (0)6 89 56 24 46 email: didier.rognan@pharma.u-strasbg.fr **************************************************************************** *********************************** David! Take a look at http://www.leadid.de/project/index.html and contact Marc directly for more info. Best, Christian BioSolveIT GmbH, An der Ziegelei 75, 53757 St. Augustin, Germany lemmen@biosolveit.de, www.biosolveit.de, Tel/Fax: +49 2241 973 66 60/88 **************************************************************************** *********************************** Dear Dr. Clark, may we draw your attention to the program SONNIA (formerly KMAP), which could be applied to the analysis of data from high-throughput screening by using neural networks? The method of using neural networks for the classification and prediction of biological activity and physicochemical properties (QSAR and QSPR) was described in several publications, among these are: * J. Sadowski, M. Wagener, J. Gasteiger, Assessing Similarity and Diversity of Combinatorial Libraries by Spatial Autocorrelation Functions and Neural Networks, Angew. Chem. Int. Ed. Engl., 34, 2674-2677 (1995) * M. Wagener, J. Sadowski, J. Gasteiger, Autocorrelation of Molecular Surface Properties for Modeling Corticosteroid Binding Globulin and Cytosolic Ah Receptor Activity by Neural Networks, J. Am. Chem. Soc., 117, 7769-7775 (1995) The program SONNIA was developed to meet the needs of chemists, as it provides many features for the visualization of chemical data. For more information about this program please visit our websites at http://212.168.36.43/software/sonnia/index.html . We would be glad to provide you with an evaluation copy of SONNIA free of charge for a test period of three months. Hope this helps, Oliver Sacher -- Dr. Oliver Sacher Molecular Networks GmbH N鋑elsbachstr. 25 91052 Erlangen, Germany Tel.: +49-9131-815668 Fax: +49-9131-815669 Email: sacher@mol-net.de Web: http://www.mol-net.de **************************************************************************** *********************************** Dear David, May be the molecular modeling package of CCG called MOE might be of help. It offers a nice binary QUASAR tool which is especially designed for HTSSAR data. May be you would like to check out the webpage: http://www.chemcomp.com/ There they have also publications for more details. Also, they offer a 3 month evaluation period of their software. Best regards, Markus. Markus Metz [metzmarkus@excite.com] **************************************************************************** *********************************** Dear David, Regarding your HTS SAR analysis tools question on CCL, [SARNavigator from Tripos] fits ideally into this category. Best wishes, Andrew Dr Andrew W Sparkes - UK Sales Executive (Tripos) Tel: (01908) 650000 Fax: (01908) 650001 Andrew Sparkes [asparkes@tripos.com] **************************************************************************** *********************************** Hi David, Pharma Algorithms has developed the Algorithm Builder package for building high-throughput screening algorithms using SAR analyses based on recursive partitioning as well as fragmental methods. I'll spare you the lengthy sales pitch and just point you to the link: http://www.ap-algorithms.com/algorithm_builder.htm and http://www.ap-algorithms.com/qsar_builder.htm Please note that Algorithm Builder contains all features of QSAR Builder. QSAR builder has numerous tools for SAR, QSAR and QSPR analysis. In most cases we will make evaluation copies available to interested users for a 45-day period. We make available a six-chapter tutorial that walks the user through the software using real data sets. Also, the following page contains PDF files of scientific posters we have presented in 2002 showing how SAR was used by our scientists in building algorithms for Human Intestinal Permeation (qualitative filter) PGP substrate specificty (qualitative) and Acute Toxicity (qualitative and quantitative) among others: http://www.ap-algorithms.com/presentations.htm Let me know if you need any more information. I would be happy to oblige. Very best regards, Darius Darius James Ross European Marketing Manager Pharma Algorithms Tauro g-ve 12 Vilnius, LT-2001 Lithuania eMail: ross@ap-algorithms.com +370 5 262 34 08 (direct) +370 5 262 37 28 (fax) www.ap-algorithms.com **************************************************************************** *********************************** Hi David, See: http://www.accelrys.com/cerius2/c2csar.html Kind regards, Richard. _________________________________________ Mr Richard Compton Office Tel. +44 1223 228 500 Office Fax. +44 1223 228 501 Direct Tel. +44 1223 228 546 Mobile +44 7740 029 611 Web. http://www.accelrys.com Email. rcompton@accelrys.com **************************************************************************** *********************************** Dear David, You may find useful the applications of Chemaxon, too: http://www.chemaxon.com Best regards, Andras Borosy Ph.D. computational chemist Andras Borosy [borosy@bluewin.ch] **************************************************************************** *********************************** **************************************************************************** *********************************** From chemistry-request@server.ccl.net Fri Dec 6 14:09:12 2002 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB6J9CA26277 for ; Fri, 6 Dec 2002 14:09:12 -0500 Received: from engr.sc.edu (wiracocha.ee.sc.edu [129.252.22.166]) by mailbox.engr.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2656.59) id T5HGD816; Fri, 6 Dec 2002 14:09:10 -0500 Message-ID: <3DF0F656.6030800@engr.sc.edu> Date: Fri, 06 Dec 2002 14:11:18 -0500 From: Hernan Figueroa Organization: University of Soth Carolina User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:0.9.4.1) Gecko/20020508 Netscape6/6.2.3 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL: Question about ONIOM Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi I apologize for asking a basic question, but I could not make the ONIOM keyword in gaussian to work. I would like to use a HF/6-31G level for C and B3PW91/LAN2DZ level for Au in a molecule that only contains Carbon and gold atoms. The next message was obtained:, using the input below: INPUT: #P ONIOM(HF/3-21G:B3PW91/LANL2DZ) SCFCYC=512 OPT Au 2.657 -1.410 0.000 Au 1.413 2.656 0.000 Au -1.413 -2.653 0.000 Au -2.658 1.406 0.000 C 0.408 0.976 0.000 Medium C 0.885 -0.579 0.000 Medium C -0.408 -0.971 0.000 Medium C -0.883 0.579 0.000 Medium ERROR MESSAGE Standard basis: 3-21G (6D, 7F) 3-21G basis sets are only available up to Xe. Error termination via Lnk1e in /usr/cluster/apps/g98a11/g98/l301.exe. Is this OK?, since I do not want to use that basis set for the gold layer I highly appreciate any help Hernan Figueroa SWGN 3A13, EE Dept University of South Carolina Columbia, SC 29208 figueroh@engr.sc.edu (803) 777-0967 From chemistry-request@server.ccl.net Fri Dec 6 16:38:37 2002 Received: from mercury.chem.northwestern.edu ([129.105.116.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB6LcbA30460 for ; Fri, 6 Dec 2002 16:38:37 -0500 Received: from localhost (hutchisn@localhost) by mercury.chem.northwestern.edu (8.11.6+Sun/8.11.3) with ESMTP id gB6LcZc01128; Fri, 6 Dec 2002 15:38:35 -0600 (CST) Date: Fri, 6 Dec 2002 15:38:35 -0600 (CST) From: Geoff Hutchison To: cc: Subject: Re: CCL:file formats/mol. medels; was:V3000 molfile format In-Reply-To: <02120613563688@itodys.jussieu.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Yes, chemistry file formats could be quite complicated and right now we have a lot of formats for specialized tasks. (e.g. ChemDraw or ISIS files for publication, CIF files for crystal results, PDB files, Molfiles, Sybyl Mol2, not to mention the slew of computational packages with their own formats.) The approach many of us have used in the past is to use translators like babel to convert from one format to another. Some data, unfortunately, might be lost, and some might have to be guessed (e.g. perception of bonds > from an XYZ file). > Last remark: any programmer should be able read and write molecular > formats (think also to read backward in large databases), without having > to pay amounts of euros or dollars to get black box routines provided > by companies (think to the catastrophic situation on Windows PC). This is exactly the point of projects like Open Babel. Read and write as many formats as possible with as little data loss as possible. (Disclaimer, I'm a developer for OB. It's still a work in progress, but improving rapidly.) Unfortunately, some file formats are entirely black boxes, completely without documentation. Not much can be done here unless there's enough pressure on companies to open their formats. Some, like MDL, have open standards, and this is wonderful. The rest either require reverse engineering or customer support/feedback to do open their formats. (IMHO, I think documented formats is entirely in the spirit of sharing scientific information.) I don't know if it's "impossible" to have one unified chemical file format, but it would certainly need to be very flexible. That's certainly the aim of CML, which may not be "perfect" yet, but seems quite useful. Just my $0.02, -Geoff -- -Geoff Hutchison Marks/Ratner Groups (847) 491-3295 Northwestern Chemistry On Fri, 6 Dec 2002 petitjean@itodys.jussieu.fr wrote: > To: CHEMISTRY@ccl.net > Subj: CCL:file formats/mol. medels; was:V3000 molfile format > > A public discussion in this list should be nice, and standards may > emerge from it. I do not believe that an universal format is possible > (too many situations), and the molecular models should be defined > before specifying any practical format. > Being a user, the first requirement that I propose is to define > one or several parameters specifying which kind of information > follows (including a release parameter). Then, a set a models > should be defined: chemical graph only, 3D only, chemical graph > plus one or more 3D, and so on... A list of widely accepted > bond types should be welcome. Some other problems: unknown atoms > or bond types, free sites for connectivity, Markush (i.e. generic) > formulas for reactions or patents, superatoms, polymers (how > many units), alloys, coefficients for components, and so on > (there are indeed much more complicated situations). > It is clear for me that specialists of chemical data banks are > able to do many useful suggestions in this area. Computational > chemistry and modeling applications have their own requirements, > and there are many others. But nothing will end before beginning. > Last remark: any programmer should be able read and write molecular > formats (think also to read backward in large databases), without having > to pay amounts of euros or dollars to get black box routines provided > by companies (think to the catastrophic situation on Windows PC). > > Michel Petitjean, Email: petitjean@itodys.jussieu.fr > ITODYS (CNRS, UMR 7086) ptitjean@ccr.jussieu.fr > 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 > 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 > http://petitjeanmichel.free.fr/itoweb.petitjean.html > > >If anyone would like to engage in a more detailed discussion about this > >issue or anything else connected with chemical structure representation > >please contact me directly at k.taylor@mdl.com. > > > -= 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 Dec 6 19:59:16 2002 Received: from marcy.nas.nasa.gov ([129.99.113.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB70xGA03471 for ; Fri, 6 Dec 2002 19:59:16 -0500 Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.6+Sun/8.11.6/NAS 8.11.6-5n) with ESMTP id gB70xFF01072 for ; Fri, 6 Dec 2002 16:59:15 -0800 (PST) Date: Fri, 6 Dec 2002 16:59:15 -0800 (PST) From: Ioana Cozmuta To: CHEMISTRY@ccl.net Subject: pdb compatibility Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, And a second question for today. I am generating a pdb file with InsightII (MSI software) and I am trying to read it in amber (leap). However it seems that there is quite a difference between the ways InsightII writes a pdb file and what amber knows to read. I am not sure but the main difference seems to be that InsightII is writing the pdb file using Brokhaven nomenclature while amber needs the IUPAC names. I am sure this is a frequent encountered problem and that there should be simple ways around. I tried to use babel and WHAT IF to correct for the differences but both failed. I would appreciate your help. Thank you, Ioana **************************************************************************** * Ioana Cozmuta, PhD * * * NASA-AMES Research Center * "Gravitation can not be held responsible* * Mail Stop 230-3 * for people falling in love" * * Moffet Field * * * phone: (650) 604-0993 * Albert Einstein* * fax: (650) 604-0350 * (1879-1955) * **************************************************************************** From chemistry-request@server.ccl.net Fri Dec 6 21:30:32 2002 Received: from marcy.nas.nasa.gov ([129.99.113.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB72UWA05873 for ; Fri, 6 Dec 2002 21:30:32 -0500 Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.6+Sun/8.11.6/NAS 8.11.6-5n) with ESMTP id gB72U8t04035; Fri, 6 Dec 2002 18:30:08 -0800 (PST) Date: Fri, 6 Dec 2002 18:30:08 -0800 (PST) From: Ioana Cozmuta To: John Bushnell cc: CHEMISTRY@ccl.net Subject: Re: CCL:pdb compatibility In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, THanks for your reply. I've already tried to use the protonate utility in amber by removing the hydrogens from the structure and letting the program add them back. The problem seems to be in the names of the heavy atoms, they seem to be incompatible as well. Ioana On Fri, 6 Dec 2002, John Bushnell wrote: > > For converting pdb files for input to Amber, use the 'protonate' > utility. It's under Miscellaneous in the Amber 7 manual. We > recently found that using this very simple translator got rid > of all sorts of problems reading Brookhaven pdb files. I hope > it works for your InsightII files (which I have no experience > with). > > HTH - John > > On Fri, 6 Dec 2002, Ioana Cozmuta wrote: > > > > > Hi, > > > > And a second question for today. > > I am generating a pdb file with InsightII (MSI software) and I am trying > > to read it in amber (leap). However it seems that there is > > quite a difference between the ways InsightII writes a pdb file and what > > amber knows to read. I am not sure but the main difference seems to be > > that InsightII is writing the pdb file using Brokhaven nomenclature while > > amber needs the IUPAC names. > > I am sure this is a frequent encountered problem and that there should be > > simple ways around. I tried to use babel and WHAT IF to correct for the > > differences but both failed. > > I would appreciate your help. > > > > Thank you, > > Ioana > > > > > > > > **************************************************************************** > > * Ioana Cozmuta, PhD * * * NASA-AMES Research Center * "Gravitation > > can not be held responsible* * Mail Stop 230-3 * for people falling in > > love" * * Moffet Field * * * phone: (650) 604-0993 * Albert Einstein* > > * fax: (650) 604-0350 * (1879-1955) * > > **************************************************************************** > > > > > > > > > > -= 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 Dec 6 21:30:52 2002 Received: from marcy.nas.nasa.gov ([129.99.113.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB72UqA05890 for ; Fri, 6 Dec 2002 21:30:52 -0500 Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.6+Sun/8.11.6/NAS 8.11.6-5n) with ESMTP id gB72UqZ04078 for ; Fri, 6 Dec 2002 18:30:52 -0800 (PST) Date: Fri, 6 Dec 2002 18:30:51 -0800 (PST) From: Ioana Cozmuta To: CHEMISTRY@ccl.net Subject: ion concentration in protein simulation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have a more general question and I've tried to look it up in the archive but I could not really get something similar. So here it is: My question relates to adding ions when simulating a large protein system. The experiments were performed using an ionic solution with a 1M concentration and with an applied electric field. I was wondering what is the usual approach in this kind of simulations: to bring the ion concentration close to the physiological number, for example? Also the solution is one of KCl so when adding ions would it be required to add in equal amounts both K+ and Cl-? I would appreciate your advice. Thank you in advance, Ioana **************************************************************************** * Ioana Cozmuta, PhD * * * NASA-AMES Research Center * "Gravitation can not be held responsible* * Mail Stop 230-3 * for people falling in love" * * Moffet Field * * * phone: (650) 604-0993 * Albert Einstein* * fax: (650) 604-0350 * (1879-1955) * **************************************************************************** From chemistry-request@server.ccl.net Fri Dec 6 21:27:01 2002 Received: from ultra.chem.ucsb.edu ([128.111.114.119]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB72R0A05804 for ; Fri, 6 Dec 2002 21:27:00 -0500 Received: from localhost (bushnell@localhost) by ultra.chem.ucsb.edu (8.12.3/8.12.3) with ESMTP id gB72QvK1019614; Fri, 6 Dec 2002 18:26:57 -0800 (PST) Date: Fri, 6 Dec 2002 18:26:57 -0800 (PST) From: John Bushnell To: Ioana Cozmuta cc: CHEMISTRY@ccl.net Subject: Re: CCL:pdb compatibility In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-milter (http://amavis.org/) For converting pdb files for input to Amber, use the 'protonate' utility. It's under Miscellaneous in the Amber 7 manual. We recently found that using this very simple translator got rid of all sorts of problems reading Brookhaven pdb files. I hope it works for your InsightII files (which I have no experience with). HTH - John On Fri, 6 Dec 2002, Ioana Cozmuta wrote: > > Hi, > > And a second question for today. > I am generating a pdb file with InsightII (MSI software) and I am trying > to read it in amber (leap). However it seems that there is > quite a difference between the ways InsightII writes a pdb file and what > amber knows to read. I am not sure but the main difference seems to be > that InsightII is writing the pdb file using Brokhaven nomenclature while > amber needs the IUPAC names. > I am sure this is a frequent encountered problem and that there should be > simple ways around. I tried to use babel and WHAT IF to correct for the > differences but both failed. > I would appreciate your help. > > Thank you, > Ioana > > > > **************************************************************************** > * Ioana Cozmuta, PhD * * * NASA-AMES Research Center * "Gravitation > can not be held responsible* * Mail Stop 230-3 * for people falling in > love" * * Moffet Field * * * phone: (650) 604-0993 * Albert Einstein* > * fax: (650) 604-0350 * (1879-1955) * > **************************************************************************** > > > > > -= 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 Dec 6 21:52:09 2002 Received: from hotmail.com ([64.4.19.42]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB72q9A06237 for ; Fri, 6 Dec 2002 21:52:09 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 6 Dec 2002 18:52:08 -0800 Received: from 61.129.121.27 by lw12fd.law12.hotmail.msn.com with HTTP; Sat, 07 Dec 2002 02:52:08 GMT X-Originating-IP: [61.129.121.27] From: "xuan xiaopeng" To: chemistry@ccl.net Subject: gw98:scff=pcm: how to specify a solvent Date: Sat, 07 Dec 2002 10:52:08 +0800 Mime-Version: 1.0 Content-Type: text/plain; charset=gb2312; format=flowed Message-ID: X-OriginalArrivalTime: 07 Dec 2002 02:52:08.0937 (UTC) FILETIME=[A25E3590:01C29D9B] Hello everybody. I want to use the PCM solvent model to calculate the structure of THF in N,N-dim ethylformamide (DMF). IN gw98 manual, I should input the dielectric constant and solvent radius. However, there are different values of DMF radius in literatures, which one is best in this calculation? And how to sepcify a solvent not list in G98 when input? Thank you for your information. Xpxuan _________________________________________________________________ 享用世界上最大的电子邮件系统— MSN Hotmail。 http://www.hotmail.com