From owner-chemistry@ccl.net Fri Aug 3 02:21:00 2007 From: "Daniil Bratashov dn2010() gmail.com" To: CCL Subject: CCL: adding hydrogens Message-Id: <-34862-070802174849-16426-qpCFFO4+pPwQSr7c/eeRQg_._server.ccl.net> X-Original-From: Daniil Bratashov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 2 Aug 2007 22:51:06 +0400 Mime-Version: 1.0 Sent to CCL by: Daniil Bratashov [dn2010]![gmail.com] On Thu, 2 Aug 2007 16:03:04 +0300 "Max Porrini mozz76(0)gmail.com" wrote: > Hi all > Does anybody know how I can add hydrogens to a system? > I've downloaded the pdb file of a enzyme and there aren't hydrogen > atoms (for instance the water molecule is formed only by the oxygen). > I'd like to saturate my system with the missing hydrogens. > Any tips will be very appreciated. > thanks a lot Ghemical can add hydrogens. WBR, Daniil Bratashov. From owner-chemistry@ccl.net Fri Aug 3 03:48:00 2007 From: "ilknur cavusoglu ilknurca##kou.edu.tr" To: CCL Subject: CCL: free descriptors software program Message-Id: <-34863-070802093239-14288-soKY9vKel0mcYy0+6Wh7Hw*o*server.ccl.net> X-Original-From: "ilknur cavusoglu" Date: Thu, 2 Aug 2007 09:32:34 -0400 Sent to CCL by: "ilknur cavusoglu" [ilknurca::kou.edu.tr] Hi everybody, Do you know any free programs that calculate molecular descriptors? Thanks for attention... Ilknur cavusoglu ilknurca###kou.edu.tr From owner-chemistry@ccl.net Fri Aug 3 05:46:01 2007 From: "Alessandro Contini alessandro.contini(0)unimi.it" To: CCL Subject: CCL: adding hydrogens Message-Id: <-34864-070803045418-15544-kqkLE4hJP9LyI48kxPU80w%server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 7bit Content-type: text/plain Date: Fri, 03 Aug 2007 09:58:23 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini+/-unimi.it] Hi, if you need to accurately protonate a protein within a certain pH and considering salinity and other parameters, the automated server H++ can be a good choice. It's fast, accurate, it provide an extesive log of the work done and, given a PDB structure file on input, H++ outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop). You only need to register at http://biophysics.cs.vt.edu/H++/ Regards Alessandro Contini Il giorno gio, 02/08/2007 alle 16.03 +0300, Max Porrini mozz76(0)gmail.com ha scritto: > Hi all > Does anybody know how I can add hydrogens to a system? > I've downloaded the pdb file of a enzyme and there aren't hydrogen > atoms > (for instance the water molecule is formed only by the oxygen). > I'd like to saturate my system with the missing hydrogens. > Any tips will be very appreciated. > thanks a lot > MP -- Dr. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Universita' degli Studi di Milano, Facolta' di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini\a/unimi.it skype alessandrocontini From owner-chemistry@ccl.net Fri Aug 3 08:41:01 2007 From: "Rajarshi Guha rguha\a/indiana.edu" To: CCL Subject: CCL: free descriptors software program Message-Id: <-34865-070803070412-9907-gtvYJwapujSrFo5NB0D/7w^^server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Fri, 3 Aug 2007 07:03:49 -0400 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Rajarshi Guha [rguha a indiana.edu] On Aug 2, 2007, at 9:32 AM, ilknur cavusoglu ilknurca##kou.edu.tr wrote: > > Sent to CCL by: "ilknur cavusoglu" [ilknurca::kou.edu.tr] > > Hi everybody, > Do you know any free programs that calculate molecular descriptors? You can try the CDK Descriptor GUI http://cheminfo.informatics.indiana.edu/~rguha/code/java/cdkdesc.html ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Psychology is merely producing habits out of rats. From owner-chemistry@ccl.net Fri Aug 3 09:16:00 2007 From: "contact.openchemsoft contact.openchemsoft%%openchemsoft.eu" To: CCL Subject: CCL: Workflow management/web services software Message-Id: <-34866-070803061001-24414-CdhhrkCwzeqZgrFqLyiwUQ[A]server.ccl.net> X-Original-From: "contact.openchemsoft" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 3 Aug 2007 11:25:14 +0200 MIME-Version: 1.0 Sent to CCL by: "contact.openchemsoft" [contact.openchemsoft**openchemsoft.eu] Hi, We will soon release Chemical Workflow Manager (CWM) , a GUI that allow to run custom workflows. Use the following link to learn about an example workflow http://www.akosgmbh.eu/cwm/index.htm Regards HansH -----Original Message----- > From: owner-chemistry * ccl.net [mailto:owner-chemistry * ccl.net] Sent: Wednesday, August 01, 2007 5:43 PM To: Himmler, Hans-Juergen Subject: CCL: Workflow management/web services software Sent to CCL by: "Andrew Colasanti" [acolasanti. * .gmail.com] I am looking into workflow management software and wanted to know about experiences and suggestions. The three that I am thinking about are 1) Taverna (taverna.sourceforge.net) 2) Knime (www.knime.org) 3) Kepler (kepler-project.org) I also know about Pipeline Pilot from SciTegic/Accelrys but the cost is prohibitive. I am also interested in the use of CDK and Openbabel within the software. The projects will be chem-/bioinformatics based. Thanks in advance Andrewhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Aug 3 10:55:00 2007 From: "Aniko Simon aniko#,#simbiosys.ca" To: CCL Subject: CCL: free descriptors software program Message-Id: <-34867-070803095045-10592-V9W5HHUpjRc0RBUzd8pU/A-x-server.ccl.net> X-Original-From: "Aniko Simon" Date: Fri, 3 Aug 2007 09:50:41 -0400 Sent to CCL by: "Aniko Simon" [aniko : simbiosys.ca] Hi Ilknur, You could try LASSO, a new 2.5 D QSAR descriptor, free for academic use. http://www.simbiosys.ca/ehits_lasso/index.html LASSO is based on our novel Interacting Surface Point Type (ISPT) descriptor and is independent of the underlying scaffold. Similarity is measured based on the surface properties of potential ligands, disregarding the 2D topology and the conformation of the ligands. This "fuzzyness" makes the descriptor suitable for scaffold hopping applications. If interested please submit a demo request. Regards, Aniko -- Aniko Simon, Ph.D. SimBioSys Inc. http://www.simbiosys.ca/ Tel: 1-416-741-4263 On Thursday 02 August 2007 09:32, ilknur cavusoglu ilknurcakou.edu.tr wrote: > Sent to CCL by: "ilknur cavusoglu" [ilknurca::kou.edu.tr] > > Hi everybody, > Do you know any free programs that calculate molecular descriptors? > Thanks for attention... > Ilknur cavusoglu > ilknurca{}kou.edu.tr > From owner-chemistry@ccl.net Fri Aug 3 13:05:01 2007 From: "Gustavo L.C. Moura gustavo]~[mercury.chem.pitt.edu" To: CCL Subject: CCL: Quantifying/estimating donor/acceptor strength Message-Id: <-34868-070803130200-26622-yGBoDJIRPx4qWZyVcjwL2g^-^server.ccl.net> X-Original-From: "Gustavo L.C. Moura" Date: Fri, 3 Aug 2007 13:01:57 -0400 Sent to CCL by: "Gustavo L.C. Moura" [gustavo!^!mercury.chem.pitt.edu] Dear CCL readers, I am looking for ways of computationally quantifying/estimating the donor/acceptor strength of groups connected to larger molecules. I want to correlate some spectral properties of these molecules with the donor/acceptor strength of these groups. If the groups I am interested were only substituted benzenes, I could rely on the Hammett sigma values. Because I am also interested in connecting heterocyclic groups to my molecules, I need to find a computational way of quantifying/estimating the donor/acceptor strength of these groups. I am aware of a property called absolute electronegativity (one half of the sum of the ionization potential with the electroaffinity of the group), but this property is unable to differentiate between the different positions of the group (meta or para substitution, for example). Does anyone in the list have any suggestion or paper that could help me with my problem? Sincerely yours, Gustavo L.C. Moura Gustavo at mercury.chem.pitt.edu From owner-chemistry@ccl.net Fri Aug 3 13:47:00 2007 From: "Shrinwantu Pal paul,+,jncasr.ac.in" To: CCL Subject: CCL:G: Siesta Message-Id: <-34869-070803133825-22129-duF2962qkoC5EMj4GI9nTw- -server.ccl.net> X-Original-From: "Shrinwantu Pal" Date: Fri, 3 Aug 2007 13:38:20 -0400 Sent to CCL by: "Shrinwantu Pal" [paul _ jncasr.ac.in] Dear esteemed suscribers, i am trying to figure out using siesta, how i can chemisorb different charged atoms onto MWCNTs. after optimization, is it possible to: see how the radial breathing modes (Raman vibrational modes) of cnt changes? i want to do this because mulliken analysis doesnt show much of charge transfer so it is difficult to understand whether this is chemisorption or physisorption (binding energies, i know). however ur expert suggestions regarding how i can use other softwares (adf/gaussian) to interpret this problem will be very helpful. also, can anyone lend me some light as to how i can perform some other calculations to understand physi/chemisorption of either neutral/charged species onto CNTs(like maybe TDDFT?) ? Thanks, Shrinwantu Pal TSU JNCASR Bangalore, India From owner-chemistry@ccl.net Fri Aug 3 14:57:00 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli ~~ gmail.com" To: CCL Subject: CCL: adding hydrogens Message-Id: <-34870-070803064343-17896-D7u3/xqXYxPsDvoyf8UYrQ]![server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_35306_3519785.1186134172103" Date: Fri, 3 Aug 2007 12:42:52 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli()gmail.com] ------=_Part_35306_3519785.1186134172103 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline AgnusLab is a freeware program that can do that. AS of not freewares, spartan can do that from the properties window, I think hydrochem can too and all the other molecular modelling programs probably :p But I would strongly suggest AgnusLab, which is a great shareware program On 8/2/07, Max Porrini mozz76(0)gmail.com wrote: > > Hi all > Does anybody know how I can add hydrogens to a system? > I've downloaded the pdb file of a enzyme and there aren't hydrogen atoms > (for instance the water molecule is formed only by the oxygen). > I'd like to saturate my system with the missing hydrogens. > Any tips will be very appreciated. > thanks a lot > MP > ------=_Part_35306_3519785.1186134172103 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline AgnusLab is a freeware program that can do that.

AS of not freewares, spartan can do that from the properties window, I think hydrochem can too and all the other molecular modelling programs probably :p

But I would strongly suggest AgnusLab, which is a great shareware program

On 8/2/07, Max Porrini mozz76(0)gmail.com <owner-chemistry{:}ccl.net> wrote:
Hi all
Does anybody know how I can add hydrogens to a system?
I've downloaded the pdb file of a enzyme and there aren't hydrogen atoms
(for instance the water molecule is formed only by the oxygen).
I'd like to saturate my system with the missing hydrogens.
Any tips will be very appreciated.
thanks a lot
MP

------=_Part_35306_3519785.1186134172103-- From owner-chemistry@ccl.net Fri Aug 3 15:32:00 2007 From: "Ivanciuc, Ovidiu I. oiivanci===utmb.edu" To: CCL Subject: CCL: free descriptors software program Message-Id: <-34871-070803135826-4116-0bBT1S5j/0UI39OvtaVgXQ{=}server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 3 Aug 2007 12:04:50 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci\a/utmb.edu] > Do you know any free programs that calculate molecular descriptors? Parameter Client http://www.vcclab.org/ http://www.vcclab.org/lab/pclient/ http://146.107.217.178/lab/pclient/ E-Dragon http://www.vcclab.org/lab/edragon/ http://146.107.217.178/lab/edragon/ MODEL - Molecular Descriptor Lab http://jing.cz3.nus.edu.sg/cgi-bin/model/model.cgi PreADMET http://preadmet.bmdrc.org/preadmet/index.php http://preadmet.bmdrc.org/preadmet/query/query1.php And if you need efficient machine learning soft for these descriptors, take a look at: http://www.support-vector-machines.org/SVM_soft.html Regards, Ovidiu Ivanciuc Sealy Center for Structural Biology and Molecular Biophysics Department of Biochemistry and Molecular Biology University of Texas Medical Branch 301 University Boulevard Galveston, Texas 77555-0857 USA http://ivanciuc.org Email: oiivanci{=}utmb.edu Email: iejmd{=}yahoo.com IEJMD: http://www.biochempress.com CoEPrA: http://coepra.org From owner-chemistry@ccl.net Fri Aug 3 16:16:01 2007 From: "Ivanciuc, Ovidiu I. oiivanci!A!utmb.edu" To: CCL Subject: CCL: Quantifying/estimating donor/acceptor strength Message-Id: <-34872-070803160932-22814-EYqXH5q29MT+r7VVkf+EGQ::server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 3 Aug 2007 15:09:11 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci(~)utmb.edu] >>>I am looking for ways of computationally quantifying/estimating >> the donor/acceptor strength of groups connected to larger molecules. If you want transferable substituent quantum indices, or Hammett type indices, see: QSAR Treatment of Electronic Substituent Effects Using Frontier Orbital Theory and Topological Parameters Jonathan J. Sullivan,* A. Daniel Jones, and Kenneth K. Tanji J. Chem. Inf. Comput. Sci., 40 (5), 1113 -1127, 2000. Group electronegativity and Fukui function studies of the substituent effects in aromatic and inorganic systems J. Korchowiec, R. F. Nalewajski International Journal of Quantum Chemistry, Volume 44, Issue 6 , Pages 1027 - 1040 Girones X, Ponec R. Molecular Quantum Similarity Measures from Fermi hole densities: modeling Hammett sigma constants. J Chem Inf Model. 2006 May-Jun;46(3):1388-93. Smith PJ, Popelier PL. Quantum chemical topology (QCT) descriptors as substitutes for appropriate Hammett constants. Org Biomol Chem. 2005 Sep 21;3(18):3399-407 Or better yet, search PubMed http://www.ncbi.nlm.nih.gov/ or Publishers' sites (Wiley,...) or Google >>>...but this property is unable to differentiate between the different >>> positions of the group (meta or para substitution, for example). Well, for mono-substituted benzenes it was easy to develop series of substituent constants for o, m, p, whereas for heterocyclic skeletons it might be difficult, due to the large diversity of reactivity and effects at various positions. This is why Hammett constants or similar substituent indices are no longer a "hot topic" in modeling molecular properties. Ovidiu Ivanciuc Sealy Center for Structural Biology and Molecular Biophysics Department of Biochemistry and Molecular Biology University of Texas Medical Branch 301 University Boulevard Galveston, Texas 77555-0857 USA http://ivanciuc.org Email: oiivanci=-=utmb.edu Email: iejmd=-=yahoo.com IEJMD: http://www.biochempress.com CoEPrA: http://coepra.org From owner-chemistry@ccl.net Fri Aug 3 18:51:00 2007 From: "Isaac Bersuker bersuker,,mail.cm.utexas.edu" To: CCL Subject: CCL: Quantifying/estimating donor/acceptor strength Message-Id: <-34873-070803145327-8522-SOUF4UOYovywegismmIGXQ=server.ccl.net> X-Original-From: Isaac Bersuker Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=KOI8-R; format=flowed Date: Fri, 03 Aug 2007 12:54:34 -0500 MIME-Version: 1.0 Sent to CCL by: Isaac Bersuker [bersuker||mail.cm.utexas.edu] We introduced an electron-donor proton-acceptor index for each atom which can be easily evaluated from the electronic structure - it may be useful for your problem, see in J. Chem. Inf. Comp. Sci. 40, 1363-1376 (2000). Regards I. B. Dr. Isaac B. Bersuker Institute for Theoretical Chemistry The University of Texas at Austin Chem & Biochem Department 1 University Station A5300 Austin, TX 78712-0165 Phone: (512) 471-4671; Fax: (512) 471-8696 E-mail: bersuker a cm.utexas.edu http://www.cm.utexas.edu/directory/isaac_bersuker/ Gustavo L.C. Moura gustavo]~[mercury.chem.pitt.edu wrote: > Sent to CCL by: "Gustavo L.C. Moura" [gustavo!^!mercury.chem.pitt.edu] > Dear CCL readers, > I am looking for ways of computationally quantifying/estimating the > donor/acceptor strength of groups connected to larger molecules. I want to > correlate some spectral properties of these molecules with the > donor/acceptor strength of these groups. > If the groups I am interested were only substituted benzenes, I could > rely on the Hammett sigma values. Because I am also interested in connecting > heterocyclic groups to my molecules, I need to find a computational way of > quantifying/estimating the donor/acceptor strength of these groups. I am aware > of a property called absolute electronegativity (one half of the sum of the > ionization potential with the electroaffinity of the group), but this property > is unable to differentiate between the different positions of the group (meta > or para substitution, for example). > Does anyone in the list have any suggestion or paper that could help me > with my problem? > Sincerely yours, > Gustavo L.C. Moura > Gustavo at mercury.chem.pitt.edu> > > From owner-chemistry@ccl.net Fri Aug 3 21:03:00 2007 From: "Curt Breneman brenec()rpi.edu" To: CCL Subject: CCL: free descriptors software program Message-Id: <-34874-070803174403-1002-8otzV09AsKl3cnDIwIMp7A[]server.ccl.net> X-Original-From: "Curt Breneman" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 3 Aug 2007 16:29:28 -0400 MIME-Version: 1.0 Sent to CCL by: "Curt Breneman" [brenec-,-rpi.edu] Please also see: http://reccr.chem.rpi.edu/software.html for several free descriptor programs, including a version of our RECON/TAE program. Cheers, Curt Breneman RPI Chemistry Director, RECCR Cheminformatics Center -----Original Message----- > From: owner-chemistry : ccl.net [mailto:owner-chemistry : ccl.net] Sent: Friday, August 03, 2007 1:05 PM To: Breneman, Curt Subject: CCL: free descriptors software program Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci\a/utmb.edu] > Do you know any free programs that calculate molecular descriptors? Parameter Client http://www.vcclab.org/ http://www.vcclab.org/lab/pclient/ http://146.107.217.178/lab/pclient/ E-Dragon http://www.vcclab.org/lab/edragon/ http://146.107.217.178/lab/edragon/ MODEL - Molecular Descriptor Lab http://jing.cz3.nus.edu.sg/cgi-bin/model/model.cgi PreADMET http://preadmet.bmdrc.org/preadmet/index.php http://preadmet.bmdrc.org/preadmet/query/query1.php And if you need efficient machine learning soft for these descriptors, take a look at: http://www.support-vector-machines.org/SVM_soft.html Regards, Ovidiu Ivanciuc Sealy Center for Structural Biology and Molecular Biophysics Department of Biochemistry and Molecular Biology University of Texas Medical Branch 301 University Boulevard Galveston, Texas 77555-0857 USA http://ivanciuc.org Email: oiivanci*utmb.edu Email: iejmd*yahoo.com IEJMD: http://www.biochempress.com CoEPrA: http://coepra.orghttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Aug 3 21:57:01 2007 From: "Sina T reli sinatureli:_:gmail.com" To: CCL Subject: CCL: Freezing Atoms Message-Id: <-34875-070803214227-24402-Dm3cfycScGxCrnSNt5I9mQ*|*server.ccl.net> X-Original-From: "Sina T reli" Date: Fri, 3 Aug 2007 21:42:24 -0400 Sent to CCL by: "Sina T reli" [sinatureli|gmail.com] Hello, I have a problem with freezing atoms in spartan. When I freeze them and perform molecular mechanics calculations, the frozen atoms move all around. I am sure that none of the atoms overlap with each other or are in extreme proximities... (Someone told me that, it could have happened due to unacceptable placement of atoms). I am afraid that it might do the same thing with SE calculations too so before moving to SE calculations I want to fix this problem and understand why it happens. I hope you can help me with this matter... Also is there any other program where we can freeze atoms and do SE calculations? Thanks