From owner-chemistry@ccl.net Tue Sep 11 01:33:01 2007 From: "Shrinwantu Pal paul^^^jncasr.ac.in" To: CCL Subject: CCL:G: long range interactions Message-Id: <-35122-070911012312-32152-kSKO6enKpedwKe585aHRQA===server.ccl.net> X-Original-From: "Shrinwantu Pal" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 11 Sep 2007 11:02:50 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Shrinwantu Pal" [paul%jncasr.ac.in] Dear esteemed fiends and colleagues, i am using gaussian 03 to predict a mechanism through irc scans and ts studies. this mechanism is guided strongly by electrostatic/coulombic interaction. Which Basis set best describes such interactions at long range? as an example: c + -XXX-(a)-(b)-YYY ----> ca-(b)YYY + XXX-(a)-bc i want (c)(+1 charge) to dock on (a)(-1 charge) and not on (b)(-0.5 charge), as i bring c closer to my molecule. i want to show two alternative ts with a-c and b-c imaginary freq. at the ts and compare the feasibilities of both pathways. Thanks in advance, Shrin JNCASR Bangalore India From owner-chemistry@ccl.net Tue Sep 11 04:08:01 2007 From: "Maxim Kholin maxim.kholin__q-pharm.com" To: CCL Subject: CCL: activity prediction software Message-Id: <-35123-070911035925-9779-wbIfHPeLgoddGzQlubMNvQ_-_server.ccl.net> X-Original-From: "Maxim Kholin" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="koi8-r"; reply-type=original Date: Tue, 11 Sep 2007 11:59:13 +0400 MIME-Version: 1.0 Sent to CCL by: "Maxim Kholin" [maxim.kholin^q-pharm.com] Hi, Igor I would like to advice you a q-Tox, that we developed in Quantum Pharmaceuticals, it is available both as a software and services. It is new approach in toxicology, it was reported recently on CMPTI-2007, among of organizers of this event are famous PASS developers. q-TOX is developed on an entirely different paradigm: we established a relation between toxicological properties of any molecule and its activity against selected classes of human proteins, rather than structural descriptors, thus avoiding difficulties of common approaches. Here are what we predict: q-TOX' toxicity endpoints: human- MRDD1 (equivalent NOAEL) human- MRTD2 human- TDLo mouse-LD50 (oral, intravenous, subcutaneous) rat-LD50 (oral, intravenous, subcutaneous, intraperitoneal) rabbit-LD50 (oral, intravenous, subcutaneous) dog-LD50 (intravenous) q-TOX' side effects prediction: Lungs, thorax, or respiration (cyanosis, dyspnea, respiratory depression, etc.) Behavioral (hallucinations, distorted perceptions, tremor, muscle contraction, ataxia, somnolence /general depressed activity/, muscle weakness, headache, toxic psychosis, etc.) Peripheral nerve and sensation (spastic paralysis with or without sensory change) Gastrointestinal (nausea or vomiting, hypermotility, diarrhea, ulceration or bleeding from stomach, etc.) Liver: hepatitis (hepatocellular necrosis, diffuse, etc.) Blood (normocytic anemia, leukopenia, hemorrhage, thrombocytopenia, eosinophilia, agranulocytosis, etc.) Kidney, ureter, and bladder (interstitial nephritis, hematuria, etc.) Cardiac (pulse rate, pulse rate increase without fall in bp, arrhythmias /including changes in conduction/, change in rate etc.). Please find more details at http://q-pharm.com/products_services/admet/drug_toxicity_prediction Kindest regards, Maxim ----- Original Message ----- > From: "Igor Filippov Contr igorf||helix.nih.gov" To: "Kholin, Maxim N " Sent: Monday, September 10, 2007 5:54 PM Subject: CCL: activity prediction software > > Sent to CCL by: "Igor Filippov [Contr]" [igorf|,|helix.nih.gov] > PASS (prediction of activity spectra) seems to be exactly what you > need: > http://www.ibmc.msk.ru/sections_en/Sect4_ProdServ/item3_soft/page.shtml > > It runs on windows and has both GUI and a command-line interface. It > takes SD files as input. > > Igor > > On Mon, 2007-09-10 at 06:39 -0400, hans himmler contact . hjhimmler.de > wrote: >> Sent to CCL by: "hans himmler" [contact||hjhimmler.de] >> I want to do some work on clustering molecular structures based on >> predicted biological activities. >> In that context I am looking for free or low cost programs that predicts >> activities. >> The program (or package) must run on windows, must provide an API or a >> command line interface and must support structure input via SDFiles (or >> smiles). >> Thanks for feedback in advance.-- > Igor Filippov [Contr] > > From owner-chemistry@ccl.net Tue Sep 11 09:31:01 2007 From: "Dan T Major majort__mail.biu.ac.il" To: CCL Subject: CCL: Data mining/clustering software Message-Id: <-35124-070911092457-13275-dy/YMzUo1WZFWld2orMTWA[A]server.ccl.net> X-Original-From: "Dan T Major" Date: Tue, 11 Sep 2007 09:24:54 -0400 Sent to CCL by: "Dan T Major" [majort^mail.biu.ac.il] Hi, We have generated tabulated data on the damage caused to nucleic acids (NA) segments (the sequence of which is known) due to exposure to various chemicals. We would like to decipher NA damage patterns out of this data. Specifically, we would like to identify short consensus NA sequences interacting specifically with certain chemicals (i.e. which consensus sequence is sensitive to which chemical, and in what typical way is a consensus sequence damaged) based on the experimental data. Can you propose a suitable software/methodology for data-mining/clustering? Many thanks From owner-chemistry@ccl.net Tue Sep 11 10:05:01 2007 From: "Wendy A Warr wendy,+,warr.com" To: CCL Subject: CCL: "ACS Meeting" reports Message-Id: <-35125-070911093535-16178-z0lVAhkLMUy769J+MWtl3g|a|server.ccl.net> X-Original-From: "Wendy A Warr" Date: Tue, 11 Sep 2007 09:35:32 -0400 Sent to CCL by: "Wendy A Warr" [wendy^^warr.com] I wanted to remind you about the August 2007 issue, based on the Spring 2007 ACS meeting. It includes accurate transcripts of 30 presentations, complete with color figures and literature references, news from almost 80 companies, and shortened press releases for the first six months of 2007. The full contents list is on the Web at http://www.warr.com/morepubs.html. Wendy Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England Tel./fax +44 (0)1477 533837 wendy[]warr.com http://www.warr.com From owner-chemistry@ccl.net Tue Sep 11 10:45:00 2007 From: "HADI behzadi behzadihadi%a%yahoo.com" To: CCL Subject: CCL:G: PDB FILE Message-Id: <-35126-070911091001-11659-HcTo80TbjVEB3eXn7vnZgA%%server.ccl.net> X-Original-From: "HADI behzadi" Date: Tue, 11 Sep 2007 09:09:58 -0400 Sent to CCL by: "HADI behzadi" [behzadihadi(_)yahoo.com] HI ALL, How can I extract pdb file for each point step in PES scan from the gaussian out? Regards From owner-chemistry@ccl.net Tue Sep 11 11:15:00 2007 From: "Jimmy Lawrence jlawrence[A]slb.com" To: CCL Subject: CCL: Method to calculate quantum dots absorption spectra and polymer capping effect Message-Id: <-35127-070911105210-2888-6On9GW8xymOeXjwl1Ej80Q###server.ccl.net> X-Original-From: Jimmy Lawrence Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 11 Sep 2007 10:52:00 -0400 MIME-version: 1.0 Sent to CCL by: Jimmy Lawrence [jlawrence::slb.com] Hi, Recently I have been wondering whether it will be possible to somehow estimate the absorption spectra of metal sulfide nanoparticles and how polymer capping effect will show up, using computational method. What will be the common procedure for doing this kind of calculation ? Can someone recommend info/books/papers ? Regards, Jimmy From owner-chemistry@ccl.net Tue Sep 11 11:50:00 2007 From: "chupvl chupvl..gmail.com" To: CCL Subject: CCL: Data mining/clustering software Message-Id: <-35128-070911110452-11061-h+Qq0spj//HnsoJ5P2AkOQ#server.ccl.net> X-Original-From: chupvl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 11 Sep 2007 19:02:03 +0400 MIME-Version: 1.0 Sent to CCL by: chupvl [chupvl^_^gmail.com] It's not clear what data you have to analyze. NA sequence or some sort damage value? Chupakhin Vladimir Dan T Major majort__mail.biu.ac.il wrote: > Sent to CCL by: "Dan T Major" [majort^mail.biu.ac.il] > Hi, > We have generated tabulated data on the damage caused to nucleic acids (NA) segments (the sequence of which is known) due to exposure to various chemicals. > > We would like to decipher NA damage patterns out of this data. Specifically, we would like to identify short consensus NA sequences interacting specifically with certain chemicals (i.e. which consensus sequence is sensitive to which chemical, and in what typical way is a consensus sequence damaged) based on the experimental data. > > Can you propose a suitable software/methodology for data-mining/clustering? > > Many thanks> > > > > From owner-chemistry@ccl.net Tue Sep 11 12:27:01 2007 From: "Ivanciuc, Ovidiu I. oiivanci(!)utmb.edu" To: CCL Subject: CCL: activity prediction software Message-Id: <-35129-070911112649-27981-htAEnkSeTC6LrSGHsG67Mw%x%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: Tue, 11 Sep 2007 10:26:40 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci]^[utmb.edu] >>>I want to do some work on clustering molecular structures >>> based on predicted biological activities. It seems that you are looking for SAR (structure-activity relationships) and QSAR (quantitative structure-activity relationships) software. For a SAR/QSAR model you need: 1. a dataset of molecules 2. structural descriptors computed for all molecules (a matrix X) 3. a machine learning software for classification (SAR) or regression (QSAR) 4. experimental values for the biological activity you want to model (a vector Y) Then the SAR/QSAR model is: Y = f(X) where f is a machine learning model with parameters determined during the training process. If you want to correlate directly the chemical structure to the biological activity, you need a "graph machine". For a review of artificial neural networks as graph machines, see the chapter: "New Neural Networks for Structure-Property Models" > from http://ivanciuc.org/iorg_bchap.html To learn more about QSAR, you may start with any review by Corwin Hansch (see Chemical Reviews/ACS). For 3D-QSAR Models, see the chapter "3D QSAR Models" from http://ivanciuc.org/iorg_bchap.html For structural descriptors see the chapter "Topological Indices" and similar reviews from the same Web page. Good choices for the machine learning models are: - support vector machines; see a list of software in the review: http://www.ivanciuc.org/Files/Reprint/Ivanciuc_SVM_CCR_2007_23_291.pdf - artificial neural networks; see SNNS - partial least squares; search Google for a MATLAB script Regards, Ovidiu From owner-chemistry@ccl.net Tue Sep 11 13:01:00 2007 From: "Ivanciuc, Ovidiu I. oiivanci:+:utmb.edu" To: CCL Subject: CCL: Data mining/clustering software Message-Id: <-35130-070911124124-18600-Iy2XdyyYuzVn9VL/n29VOg%a%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: Tue, 11 Sep 2007 11:41:16 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci^-^utmb.edu] >>>We have generated tabulated data on the damage caused to nucleic acids (NA) >>> segments (the sequence of which is known) due to exposure to various chemicals. >>>We would like to decipher NA damage patterns out of this data. >>> Specifically, we would like to identify short consensus NA sequences >>> interacting specifically with certain chemicals Your problem is a typical structure-activity relationship (SAR) modeling. The most important part is to find a good translation of the NA sequence and chemical data into numerical descriptors. For the machine learning algorithm that relates the chemical structure to the biological activity, you may use: a. an artificial neural network - see SNNS b. support vector machines - see http://www.ivanciuc.org/Files/Reprint/Ivanciuc_SVM_CCR_2007_23_291.pdf Regards, Ovidiu From owner-chemistry@ccl.net Tue Sep 11 13:35:01 2007 From: "Ron Cook cookrl]=[tda.com" To: CCL Subject: CCL: Data mining/clustering software Message-Id: <-35131-070911120423-26212-HcTo80TbjVEB3eXn7vnZgA{}server.ccl.net> X-Original-From: "Ron Cook" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 11 Sep 2007 09:31:29 -0600 MIME-Version: 1.0 Sent to CCL by: "Ron Cook" [cookrl/./tda.com] Try the freely downloadable datamining software WEKA and also buy the book "Data Mining: Practical Machine Learning Tools and Techniques" which has a chapter on the use of WEKA for datamining along with a good general background for datamining techniques Ronald Cook cookrl,tda.com -----Original Message----- > From: owner-chemistry,ccl.net [mailto:owner-chemistry,ccl.net] Sent: Tuesday, September 11, 2007 7:25 AM To: Cook, Ronald L Subject: CCL: Data mining/clustering software Sent to CCL by: "Dan T Major" [majort^mail.biu.ac.il] Hi, We have generated tabulated data on the damage caused to nucleic acids (NA) segments (the sequence of which is known) due to exposure to various chemicals. We would like to decipher NA damage patterns out of this data. Specifically, we would like to identify short consensus NA sequences interacting specifically with certain chemicals (i.e. which consensus sequence is sensitive to which chemical, and in what typical way is a consensus sequence damaged) based on the experimental data. Can you propose a suitable software/methodology for data-mining/clustering? Many thankshttp://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 Tue Sep 11 14:11:01 2007 From: "Adam Tenderholt atenderholt]~[gmail.com" To: CCL Subject: CCL:G: PDB FILE Message-Id: <-35132-070911135731-19409-GYHusExZavBa6ZJ3UjxeaA^server.ccl.net> X-Original-From: "Adam Tenderholt" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 11 Sep 2007 10:57:23 -0700 MIME-Version: 1.0 Sent to CCL by: "Adam Tenderholt" [atenderholt ~~ gmail.com] Hi, There are several programs that probably will do what you want. PyMOlyze (http://pymolyze.sourceforge.net/) will let you view the structure and coordinates at each point found in a Gaussian calculation. Other calculation packages are also supported; see the website for more information. You can save a structure as a PDB, XYZ, or a couple other formats. In addition, you can do simple manipulations such as center the molecule at an atom, align a bond to an axis, or rotate the molecule such that three atoms are in the same plane. Molden also lets you read in Gaussian (and other) logfiles and lets you save the structure at each point found. It also has a z-matrix editor and a good interface for monitoring structural parameters during an optimization (and presumably an IRC). Finally, If you're familiar with programming, especially in Python, cclib and openbabel can be combined to do what you want if the above aren't sufficient. (PyMOlyze actually uses these two libraries.) Adam On 9/11/07, HADI behzadi behzadihadi%a%yahoo.com wrote: > > Sent to CCL by: "HADI behzadi" [behzadihadi(_)yahoo.com] > HI ALL, > How can I extract pdb file for each point step in PES scan from the gaussian out? > Regards> > > > From owner-chemistry@ccl.net Tue Sep 11 14:45:00 2007 From: "Boyd, D. boyd~~chem.iupui.edu" To: CCL Subject: CCL: activity prediction software Message-Id: <-35133-070911142533-31541-nDdxlT4yoLO+/uSz8p7RKg_-_server.ccl.net> X-Original-From: "Boyd, D." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 11 Sep 2007 13:28:10 -0400 MIME-Version: 1.0 Sent to CCL by: "Boyd, D." [boyd#,#chem.iupui.edu] Another excellent review of artificial neural networks is: K. Peterson, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 2000, Vol. 16, pp. 53-140. Artificial Neural Networks and Their Use in Chemistry. From owner-chemistry@ccl.net Tue Sep 11 15:36:01 2007 From: "N. Sukumar nagams###rpi.edu" To: CCL Subject: CCL: Data mining/clustering software Message-Id: <-35134-070911151332-9533-6H8L5eEAL3mq4Z4vtBwC3Q=server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Tue, 11 Sep 2007 14:01:35 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams%rpi.edu] For nucleic acid descriptors, see the DIXEL model: http://reccr.chem.rpi.edu/Software/Dixel/dixel-index.html Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute http://reccr.chem.rpi.edu/ ==============Original message text=============== On Tue, 11 Sep 2007 12:41:16 EDT "Ivanciuc, Ovidiu I. oiivanci:+:utmb.edu" wrote: Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci^-^utmb.edu] >>>We have generated tabulated data on the damage caused to nucleic acids (NA) >>> segments (the sequence of which is known) due to exposure to various chemicals. >>>We would like to decipher NA damage patterns out of this data. >>> Specifically, we would like to identify short consensus NA sequences >>> interacting specifically with certain chemicals Your problem is a typical structure-activity relationship (SAR) modeling. The most important part is to find a good translation of the NA sequence and chemical data into numerical descriptors. For the machine learning algorithm that relates the chemical structure to the biological activity, you may use: a. an artificial neural network - see SNNS b. support vector machines - see http://www.ivanciuc.org/Files/Reprint/Ivanciuc_SVM_CCR_2007_23_291.pdf Regards, Ovidiuhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Tue Sep 11 20:03:00 2007 From: "Kaci Tizi_Ouzou kaci.tiziouzou-*-gmail.com" To: CCL Subject: CCL:G: G03: Restarting optimization and SCF Message-Id: <-35135-070911182244-10855-Ao4JARpL9utWT1GPLSlehA(_)server.ccl.net> X-Original-From: "Kaci Tizi_Ouzou" Content-Type: multipart/alternative; boundary="----=_Part_7263_14969827.1189545505654" Date: Tue, 11 Sep 2007 15:18:25 -0600 MIME-Version: 1.0 Sent to CCL by: "Kaci Tizi_Ouzou" [kaci.tiziouzou+*+gmail.com] ------=_Part_7263_14969827.1189545505654 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi All, I am having a computation issue with Gaussian 03. I have a calculation for which BOTH geometry optimization and SCF do not coonverge. Even though I have upped MAXCYC of the SCF to 1024, the convergence is still not ok. So my question is: If the SCF does not converge WITHIN a geometry optimization run, should I use: # blah blah OPT(restart, MAXCYC=100) <-- Restarting only the Optimization OR # blah blah OPT( restart, MAXCYC=100) SCF(restart, MAXCYC=1024) <--- This does not seem to work though!! Any help will be much appreciated. Kass ------=_Part_7263_14969827.1189545505654 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi All,
 
 
I am having a computation issue with Gaussian 03.
 
I have a calculation for which BOTH geometry optimization and SCF do not coonverge.
 
Even though I have upped MAXCYC of the SCF to 1024, the convergence is still not ok. So my question is:
 
If the SCF does not converge WITHIN a geometry optimization run, should I use:
 
# blah blah  OPT(restart, MAXCYC=100) <-- Restarting only the Optimization
 
OR
 
# blah blah OPT( restart, MAXCYC=100) SCF(restart, MAXCYC=1024) <--- This does not seem to work though!!
 
 
Any help will be much appreciated.
 
 
Kass
 
 
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