From owner-chemistry@ccl.net Thu May 24 05:12:00 2007 From: "James Robinson James.Robinson|prosonix.co.uk" To: CCL Subject: CCL:G: Gaussian Problems..ouch... Message-Id: <-34340-070523140703-18741-4WsU4UxCjX2QjprIVdbniA.@.server.ccl.net> X-Original-From: "James Robinson" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 23 May 2007 18:27:06 +0100 MIME-Version: 1.0 Sent to CCL by: "James Robinson" [James.Robinson-*-prosonix.co.uk] Jeff, Your rant below is warranted. It did take me some time to learn the discipline of z-matrices, however, once mastered I don't like doing Cartesian or other such silly stuff. Gamess is a good simple package, the input syntax is wonderful as one is forced to try and understand what one is doing! Dalton and NWChem seem to be for aca-flaming-demics..I am not an aca-flaming-demic..wonder how much NWChem for industrial people is? The biggest problem I now have with younger and less experienced staff is that they seem to think that they can draw something, click "optimise" and the resultant structure has significance..I do wish people would try to understand more about how computational results can compliment and even sometimes guide experiments..or it is now the case that computational chemistry is seen as cool and an escape from wearing a lab-coat..it is easier to sit in front of a keyboard than actually do some work nowadays.. Rant over. Dr James J Robinson -----Original Message----- > From: owner-chemistry---ccl.net [mailto:owner-chemistry---ccl.net] Sent: 23 May 2007 16:28 To: James Robinson Subject: CCL:G: Gaussian Problems Sent to CCL by: Jeff Hammond [jeff.science!=!gmail.com] Recently, it seems that nearly half the messages on this listserve are for Gaussian technical support. To this, I have a few comments: 1. If Gaussian isn't working for you, that's either your fault or Gaussian's. That means either you RTFM or email help.---.gaussian.com. Stop dumping your technical support problems on a list meant to serve the whole computational chemistry community, not just those who are foolish enough to pay for second-rate code. 2. Gaussian should have their own user listserve. They don't, probably because of the cost of hardware and maintenance. Funny how all the free codes can afford this but Gau$$ian cannot. Why don't you tell them to set one up next time you renew your draconian license. 3. Consider saving yourself time and money by going online, downloading a free code which does what you want and comes with great tech support and a user listserve. To preempt the most common objection to using codes other than Gaussian: if you cannot figure out how to make an input file in a format other than Gaussian's, you are too stupid to be a computational chemist. By not using Gaussian, you'll be paying yourself $4,000 to learn a new input format. Here are three codes which can probably replace Gaussian for 99% of its users: Dalton http://www.kjemi.uio.no/software/dalton/dalton.html GAMESS http://www.msg.ameslab.gov/GAMESS/gamess.html NWChem http://www.emsl.pnl.gov/docs/nwchem/nwchem.html Use the scientific brain you claim to have by being on this list and do the math: using Gaussian does not make financial or scientific sense. Jeffhttp://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 Thu May 24 06:46:00 2007 From: "Herbert Fruchtl herbert.fruchtl .. st-andrews.ac.uk" To: CCL Subject: CCL: NWChem (was: Gaussian Problems) Message-Id: <-34341-070524064300-3455-zOwLTmhGM9k2N/kC23QQCg#%#server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 24 May 2007 11:42:17 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl##st-andrews.ac.uk] > Dalton and NWChem seem to be for > aca-flaming-demics..I am not an aca-flaming-demic..wonder how much > NWChem for industrial people is? As far as I know it's free, as long as you are not in a country that the US government doesn't like. The major problem with NWChem is that it's painfully slow for standard applications (i.e DFT) on one or a few processors. Where it's unbeatable is really large calculations on really large parallel computers. And it has a very logical input structure, so it's easy to learn. Herbert -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Thu May 24 09:04:01 2007 From: "Jan Labanowski janl/a\speakeasy.net" To: CCL Subject: CCL: June 21-22, OpenEye European Science Meeting in Sheffield Message-Id: <-34342-070524090237-2895-VGJTCyeh4OrfszRPSnIOFQ .. server.ccl.net> X-Original-From: "Jan Labanowski" Date: Thu, 24 May 2007 09:02:34 -0400 Sent to CCL by: "Jan Labanowski" [janl .. speakeasy.net] Dear Colleague, The final program for OpenEye's first European science meeting, which will take place on the 21st and morning of the 22nd of June in Sheffield, England, is now available. We have scheduled three sessions: Thursday morning will be on chemical information and modeling, Thursday afternoon on structural information, and Friday morning on electrostatics. Thursday evening will be the keynote lecture given by Dr. Dave Timms recently retired from AstraZeneca. There will also be opportunities to meet the developers of OpenEye software and learn about our approach to modeling. I think the line-up is very strong for this first European meeting and hope you can join us. Look forward to seeing you in Sheffield, Anthony Nicholls, President and CEO OpenEye Scientific Software, Inc. --------- Notes and reminders: - EuroCUP 2007 online registration: http://www.eyesopen.com/cgi-bin/eurocup_reg - Registration is FREE and remains open. - Reserve EARLY at the conference hotel as availability is limited! The conference hotel is: Hilton Sheffield Hotel Victoria Quays, Furnival Road Sheffield, S47YA, UK tel: 44 (0) 114 252 5500 fax: 44 (0) 114 252 5511 email: nicholas.goldwasser[A]hilton.com Please request the special "OpenEye EuroCUP" group rate (meals included) of 140. ----------------------- Thursday, June 21 8:00 Registration / Tea, coffee, pastries 8:45 Welcoming remarks, Anthony Nicholls, OpenEye Morning : Chemical information and modeling 9:00 "Virtual Exploration of Chemical Space by Database Generation", Jean-Louis Reymond, University of Berne 9:40 "Breaking the Language Barrier: Chemical Nomenclature around the Globe", Roger Sayle, OpenEye 10:10 Morning break 10:30 "Using Pareto Methods to Evolve Structure-activity Relationships", Val Gillet, University of Sheffield 11:00 "Communicating Chemical Information in a Research Organization", Joe Corkery, OpenEye 11:30 "Further Adventures in Shape Space", Paul Hawkins, OpenEye 12:00 Lunch 13:15 OpenEye Product Review - Ligand-based design, Paul Hawkins, OpenEye Afternoon : Structural information 14:15 "Structure and Property Predictions for Molecular Organic Molecules: Progress and Blind Tests", Graemer Day, University of Cambridge 14:55 "Computed Crystal Energy Landscapes for the Prediction and Understanding of Polymorphism", Sally Price, University College London 15:25 Afternoon break 15:45 "Validating Crystallographic Ligands", Brian Kelley, OpenEye 16:15 "Exploiting Ligand Conformations in Drug Design", Jonas Bostrm, AstraZeneca 16:45 "When Pigs Won't Fly...", Gerard Kleywegt, Uppsala University 17:30 Keynote lecture: "Drug Discovery: Research or Process?", Dave Timms, AstraZeneca (retired) 19:00 Conference Dinner --------- Friday, June 22 8:15 Tea, coffee, pastries Morning: Electrostatics 9:00 "Piling Pelion on Ossa: the Tangled Web of Tautomer Preference", Peter Taylor, AstraZeneca (retired) 9:40 "Five Years of Field Comparisons and Other Dangers of Letting Chemists & Physicists Talk", Geoff Skillman, OpenEye 10:10 Morning break 10:30 "The Sheffield Solvation Model and Other Stunningly Simple Ideas to Improve Molecular Modeling", Andrew Grant, AstraZeneca 11:00 "Protein Electrostatics, Function, and Environment", Jim Warwicker, University of Manchester 11:30 "Physically Correct Charges. Think You Use Them? Think Again", Anthony Nicholls, OpenEye 12:00 Concluding remarks, Anthony Nicholls, OpenEye Close --------------------- Available Abstracts Virtual Exploration of Chemical Space by Database Generation Jean-Louis Reymond, University of Berne, Switzerland Organic chemisty is the study of molecules made by forming covalent bonds between atoms of carbon, hydrogen, oxygen, nitrogen, halogens, and a few other elements (S, P, Si). The ensemble of all possible molecules forms the so-called chemical universe, or chemical space. Our aim is to explore chemical space in depth by exhaustive generation in silico, going beyond what nature and chemists have synthesized or imagined to date. We have generated a database of all molecules of C, N, O, F up to 11 atoms (H's are added to complement valency) possible under consideration of chemical stability and synthetic feasibility rules. The database illuminates the scope of organic chemistry and points to new chemotypes with promising predicted properties. We are also developing a strategy that goes beyond the 11 atom limit of exhaustive listing and explores chemical space systematically up to molecules of ca. 50 atoms. Breaking the Language Barrier: Chemical Nomenclature around the Globe Roger Sayle, OpenEye The use of chemical compound names remains the primary method for conveying molecular structures between chemists and researchers. In research articles, patents, chemical catalogues, government legislation and textbooks, the use of IUPAC and traditional compound names is universal, despite efforts to introduce more machine-friendly representations such as identifiers and line notations. Fortunately, advances in computing power now allows chemical names to be parsed and generated (read and written) with almost the same ease as conventional connection tables. A significant complication, however, is that although the vast majority of chemistry uses English nomenclature, a significant fraction is in other languages. This complicates the task of filing and analyzing chemical patents, purchasing from compound vendors and text mining research articles or web pages. This talk describes the issues with manipulating chemical names in various languages, including British, American, Spanish, Swedish and Japanese, and describes the current state-of-the-art in tools to simplify the process. Communicating Chemical Information in a Research Organization Joe Corkery, OpenEye Pharmaceutical and biotech research organizations are relatively heterogeneous, comprised of many distinct groups of users with differing expectations, experience, methodologies, priorities, and even IT infrastructure. The communication of chemical information between these groups is critical to the discovery process but is often limited by these constraints. Chemical information refers to not only chemical structures, but also to their associated "meta" information such as prioritization, hit lists, user annotations, as well as calculated and measured properties. Addressing this challenge has required extensive research, experimentation and innovation on many fronts including navigating the heterogeneity of both hardware and the user, as well as the many varying methodologies of data communication and presentation. We have attempted to tackle these issues with the development of VIDA and Vivant. VIDA addresses the challenges of heterogeneity by providing the same easy-to-use intuitive interface to a powerful visualization application across multiple platforms (Microsoft Windows, Linux/Unix, and Mac OS X). The interface takes advantage of widely accepted interface paradigms in order to focus on use by many different types of users instead of just a narrowly defined subset of specialists. Vivant addresses the challenges of communication by specifically leveraging the established power of Microsoft PowerPoint and the World Wide Web as communication mediums in order to present not only the chemical structures (as visualized in VIDA) but also the "meta" information generated for them based on user interactions with those compounds. Given the resources now available, do they make a difference? Potential tests will be discussed. Further Adventures in Shape Space Paul Hawkins, OpenEye It has been a long-held assumption in ligand-based virtual screening that the bioactive conformation of a molecule is privileged and superior performance should be obtained when using such a conformation. A parallel assumption has been that extensive sampling of the conformational space of database molecules is necessary to obtain optimal performance. Both of these assumptions will be critically assessed in the case when ligand-based virtual screening is carried out in shape space. Structure and Property Predictions for Molecular Organic Molecules: Progress and Blind Tests Graemer Day, University of Cambridge Computational methods for the prediciton of molecular organic crystal structures have been developing rapidly over the past 2 decades and many promising results have been reported. Evaluations of current methods for structure prediction are presented, including blind tests of crystal structure prediciton. Three such blind tests have been run over the past 8 years, as an objective test of current capabilities; the organisation and results of these are presented. As well as the ambitious aim of structure prediction, methods have been improving for the prediciton and understanding of physical properties (including mechanical and dynamic properties) of organic crystals with known structure; these methods, and their performance, are also discussed. Computed Crystal Energy Landscapes for the Prediction and Understanding of Polymorphism Sally Price, University College London Contrasting the thermodynamically feasible crystal structures with those that are experimentally known, can either confirm that an experimental polymorph screen is effectively complete, or provide structures to target by other crystallisation methods and generally help rationalise polymorph and solvate formation. This will be illustrated by a range of examples, including cases of prior prediction of polymorphs, to show how computational modelling is progressing in the range of molecules for which useful crystal energy landscapes can be computed. Validating Crystallographic Ligands Brian Kelley, Jim Nettles, and Greg Warren, OpenEye A daunting task for computational chemists is the validation of crystallographic complexes. Data quality used to determine structures can be quite poor forcing a decision of whether to use the current low quality model or to invest in attempts to collect higher quality data. Here, we present a collection of techniques used by crystallographers and modelers to validate structures. Crystallographic techniques include real space correlation[1] and Difference of Difference (DOD) [2] method. These techniques are juxtaposed with techniques familiar to computational chemists such as contact surfaces, strain energy and clash potentials. Finally we show, using examples from the RSCB[3], that in many cases the initial poor ligand structure can be replaced with a chemically sensible and low-strain conformation that is equivalently fit to the crystallographic data. [1] Jones, T.A. Acta. Cryst , 1991, A47, 110-119. [2] Nettles, J. H., Science 2004, 305, 866-869 [3] Perola, E.; Charifson, P. S. J. Med. Chem. 2004, 47, 2499-2510. Exploiting Ligand Conformations in Drug Design Jonas Bostrm, AstraZeneca Drug discovery requires the analysis of increasing amounts of data. Computational chemistry plays a role in organizing and interpreting such data with the goal of making predictions. More specifically molecular design involves coupling predictions about how modifications to molecular structure are manifested in terms of changes to experimental properties. The dominant methods of establishing similarities between molecules and their relationships to measured data are based on the local connectivity of atoms, and as such reflect how molecules have been historically drawn in medicinal chemistry. A better physically founded approach to molecular modeling is to consider the three dimensional (3D) shape of molecules. However, it has proved difficult to fully realize all of the potential advantages of 3D based techniques, in part due to the difficulty of obtaining good descriptions of the conformations of molecules. A particular challenge is in determining the conformation of a molecule when it is bound to a given biological target, the so-called bioactive conformation. Despite the numerous approximations involved in both modeling the energetics of conformers and the methodologies involved in searching conformational space, it has been shown that the insights from conformational analysis can contribute to drug discovery projects. This will, for example, be illustrated by the design of a novel class of cannabinoid (CB1) receptor antagonists for the treatment of obesity. When Pigs Won't Fly... Gerard Kleywegt, Uppsala University Once upon a time, in the land of the unicorn, where every rainbow had a pot of gold at both ends, where everybody was beautiful, healthy and happy, and where pigs could fly, all protein crystallographers were brilliant scientists who never made any mistakes. Meanwhile, back on Earth, the situation is slightly less favourable. As the recent debacle with the ABC transporter structures has (once again!) shown, the mere fact that something (say, a hot crystal structure) is published in Nature or Science is uncorrelated to its correctness. A few examples of the mistakes that crystallographers can make will be given, and simple ways in which non-experts can assess the overall reliability of structures will be discussed. However, even when the overall structure is reliable, some details may not be (much like Orwell's pigs, all residues are equal, but some residues are more equal than others). Of particular interest in this respect are the protein residues that interact with substrates or inhibitors and the interacting molecules themselves. It will be shown (with some amusing examples) that the structures of these "size-challenged" molecules when determined in complex with biomacromolecules are at times rather less reliable than those of their big bio brethren. Obviously, these observations have important implications for users of protein structures. For one thing, these structures should be treated with healthy scepticism rather than reverence. The best way to assess the reliability of critical aspects of a structure (ligand, active-site residues, metal-binding site, interface residues, etc.) is to inspect the experimental electron density maps. Our efforts to provide such maps, and information derived from them, for all crystal structures for which structure factors have been deposited with the PDB will be discussed. They have resulted in EDS - the Uppsala Electron Density Server (http://eds.bmc.uu.se/). If time permits, a new tripendicular server called ValLigURL (which is, like, totally pronounced "Valley Girl" - duh!) will also be described. It can be used to answer various totally sluggin' questions about ligand conformations in macromolecular crystal structures, including: Has this conformation of my favourite ligand, like, been observed before in the PDB? Which PDB entries contain my favourite ligand but in a, like, way different conformation (somebody - gag me with a spoon!)? How do the bond lengths and angles of, like, my favourite ligand compare to the ideal values (taken from MSDchem) or to the values found in the same ligand in other gnarly PDB entries? Which tubular PDB entry contains a copy of my favourite ligand that has the best bond lengths and angles (so that I can, like, totally use that entry as a starting point for my modelling work)? Piling Pelion on Ossa: the Tangled Web of Tautomer Preference Peter Taylor, AstraZeneca (retired) Despite the mass of experimental information that has accumulated on tautomerism over the past half century, there has been no serious attempt so far to systematise the data in the interests of a predictive methodology. Since tautomer preference is phase dependent the choice of standard phase is crucial, and we opt for water as the universal biological medium. We shall demonstrate that removing the distortions entailed in the inevitable use of model compounds can result in such improved internal consistency that hitherto undetected correlations become visible. We go on to analyse one of many cases is which the use of additive assumptions has allowed the identification and quantification of an important perturbing factor whose use can aid prediction in a wide variety of contexts. Five Years of Field Comparisons and Other Dangers of Letting Chemists & Physicists Talk Geoff Skillman, OpenEye Molecular similarity, whether computational or in the imagination of a chemist, has a long and distinguished history of success in medicinal chemistry. In the 1980s and 1990s, a chemistry perspective, in which atom typing played a prominent role, dominated both 2D and 3D similarity approaches (e.g. MACCS, Catalyst). Coulombic-field similarity was also introduced in the early 1990s (e.g. CoMFA) and Coulombic fields were later reduced to atom-type related field points that allowed easier alignment and comparison (e.g. Cresset). In 2002 OpenEye introduced fast physics-based methods to both align and directly compare electrostatic fields of small molecules in water (Anthony Nicholls, Cup II). Here we will present our experience over the past five years and show that careful consideration of chemistry details such as variable resolution conformer exploration, high quality partial charges, proper ionization and tautomer states, physiologic salt concentrations and a justifiable interaction model are both necessary and sufficient to achieve outstanding performance from solvated electrostatic-field comparisons. Sheffield Solvation Model and Other Stunningly Simple Ideas to Improve Molecular Modeling Andrew Grant, AstraZeneca There are two ways to model a solute in water. Choose a force-field, apply massive computing power and wait a long time. Or choose an implicit solvent model, enlist any computer made in the last thirty years and get an answer potentially every bit as good in a fraction of the time. How small a fraction? Typically a million-fold or more. Given the enormous difference in speed between explicit and implicit models, is there really any need for yet faster implicit solvent models? This talk will suggest there is. The Sheffield Solvation model, named for its point of origin, is dramatically faster than other implicit solvent models, allowing, for example, on-the-fly calculation of conformational and vibrational entropies, important components often ignored in physical property prediction. In addition it is competitive in accuracy and trivial to implement with simple, analytic gradients. The historical development of the model will be presented, such as aspects of the more substantial model from which it was derived and also the light it sheds on the over-parameterisation of certain other implicit solvent models. Finally, simple ways will be suggested to extend Sheffield to achieve greater accuracy and extensibility. Protein Electrostatics, Function, and Environment Jim Warwicker, University of Manchester We develop methods to calculate pH-dependent properties for biological molecules, finding that a combination of Finite Difference Poisson-Boltzmann and Debye-Huckel provides a good and relatively fast approximation in many cases. We look for correlations between calculations/predictions and environmental properties, such as subcellular location. Revisiting the widely discussed topic of charges and thermostability, although we predict greater stabilisation from ionisable groups for hyperthermophile proteins, this does not correlate with the numbers of such groups. Since these numbers are also larger for hypothermophile proteins, we infer that at least two effects are in operation (stability and solubility). Shape-based protein electrostatics has seen a minor revival in the era of Structural Genomics, from addressing issues such as predictions of enzyme/non-enzyme or nucleic acid-binding. These are relatively trivial implementations of the complexity implicit in detailed charge/shape analysis. A more lasting contribution would be the development of algorithms to match 3D structures (proteins etc) to detailed functional classes, at least for enzymes. Physically Correct Charges. Think You Use Them? Think Again Anthony Nicholls, OpenEye The point charges we are familiar with in modeling are: (a) under-determined and not physically observable (b) try to account for both electrostatic potentials and polarization, the latter through the ubiquitous application of over-polarized basis sets popularized by the likes of Kollman, Karplus and others. I will illustrate why charges can not do both but that the use of an actual physical observable, the dielectric constant, resolves matters, predicts a new and reasonable constant for solvated systems, unifies a wide range of charge and uncharged systems, solves some old problems, such as halide transfer energies, while posing interesting new conundrums. From owner-chemistry@ccl.net Thu May 24 09:39:00 2007 From: "frisch..:..gaussian.com (Michael Frisch)" To: CCL Subject: CCL:G: Gaussian Problems, really another misrepresentation of Gaussian, Inc.'s policies Message-Id: <-34343-070524011926-25299-vuw0iiSFXXZWZYxzEDJfdg.:.server.ccl.net> X-Original-From: frisch-#-gaussian.com (Michael Frisch) Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 24 May 2007 00:46:08 -0400 Mime-Version: 1.0 Sent to CCL by: frisch::gaussian.com (Michael Frisch) On Wed, May 23, 2007 at 05:26:47PM -0400, Caroline M. Taylor cmtaylor---mtu.edu wrote: > > Sent to CCL by: "Caroline M. Taylor" [cmtaylor- -mtu.edu] > Hello, all. > > "excessively harsh and severe," a definition which I do think applies to > the Gaussian licensing policies (i.e. if you dare to use something else, > we'll take it away from you). > There is no such policy and there never has been. Gaussian doesn't license it's software to people who are developing directly competing software, but there is no restriction on what other software customers use. Mike Frisch From owner-chemistry@ccl.net Thu May 24 10:44:00 2007 From: "Stephen Wilson quantumsystems ~ gmail.com" To: CCL Subject: CCL: Quantum Systems in Chemistry & Physics XII Message-Id: <-34344-070524104215-20411-pScoQpqwChOA5Ddn4UHZrA()server.ccl.net> X-Original-From: "Stephen Wilson" Date: Thu, 24 May 2007 10:42:11 -0400 Sent to CCL by: "Stephen Wilson" [quantumsystems*|*gmail.com] Early bird registration for the QSCP-XII workshop remains open for just one week. The 2007 Workshop will include sessions on: Concepts and Methods in Quantum Chemistry and Physics; Correlation, Relaxation and Relativity Treatments Molecular Structure and Spectroscopy; Valence Theory, Nuclear Motion, Vibronic Effects Atoms and Molecules in Strong Electric and Magnetic Fields Condensed Matter; Complexes and Clusters; Surfaces and Interfaces Molecular and Nano-Materials and Electronics Reactive Collisions and Chemical Reactions Computational Chemistry, Biochemistry and Chemical Physics Details of the registration procedure are to be found on the webpage: http://quantumsystems.googlepages.com/expressionofinterest A list of expected participants can be found at http://quantumsystems.googlepages.com/2007qscpparticipants Stephen Wilson quantumsystems%a%gmail.com From owner-chemistry@ccl.net Thu May 24 12:20:00 2007 From: "Richard L Wood rwoodphd[A]msn.com" To: CCL Subject: CCL: Pharmacophore modeling Message-Id: <-34345-070524121901-17042-pKOSwMJQ8w/jzq/xZm2oZA_._server.ccl.net> X-Original-From: "Richard L Wood" Date: Thu, 24 May 2007 12:18:58 -0400 Sent to CCL by: "Richard L Wood" [rwoodphd=msn.com] Hi all, Do any of you know of any FREE programs to do pharmacophore modeling that wil run under Windows? I'm currently using Sybyl under Linux, but I'd like to try something else. If not Windows, Linux would be alright, but I'd prefer that it run under Windows. The bottom line is that it must be free. Richard From owner-chemistry@ccl.net Thu May 24 13:07:00 2007 From: "Kalyan chaitanya kalyanpulipaka[]gmail.com" To: CCL Subject: CCL: HADDOCK installation Message-Id: <-34346-070524125726-1666-ElOnE5D8K/L9qiC+bqEByw|*|server.ccl.net> X-Original-From: "Kalyan chaitanya" Content-Type: multipart/alternative; boundary="----=_Part_100947_24436336.1180025818752" Date: Thu, 24 May 2007 22:26:58 +0530 MIME-Version: 1.0 Sent to CCL by: "Kalyan chaitanya" [kalyanpulipaka- -gmail.com] ------=_Part_100947_24436336.1180025818752 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear andrea, Thank you for your response, now I could install haddock i.e i could source it successfully, not only haddock, but CNS and python but what i didn't understand is 1. what is the significance of ARIA, should we install ARIA to run haddock. 2. i learn that run.CNS is the file where we have make the changes to run haddock and should execute that file, but where should we execute it, is it in python, CNS or haddock directories.... 3. in this process of installation i didn't give the path of python, where should we give that. and also i apologise for my delay in gratitude for ur response. Thank you in advance, P.Kalyan On 5/22/07, andrea spitaleri spitaleri.andrea%a%hsr.it < owner-chemistry],[ccl.net> wrote: > > > Sent to CCL by: andrea spitaleri [spitaleri.andrea_._hsr.it] > Hi, > I am actually using HADDOCK and it quite easy to install it: > 1. install python & cns > 2. copy somewhere the haddock package > 3. set the environment > that's it! > for more information, just have look to the HADDOCK mailing list > > Regards > > andrea > > Kalyan chaitanya kalyanpulipaka###gmail.com wrote: > > Dear all, > > > > Is there any one who have worked with HADDOCK for protein-protein > > docking, iam facing a challenge with installation of the same > software.... > > > > Thanks in advance, > > > > P.Kalyan. > > -- > ------------------------------- > Andrea Spitaleri PhD > Dulbecco Telethon Institute > c/o DIBIT Scientific Institute > Biomolecular NMR, 1B4 > Via Olgettina 58 > 20132 Milano (Italy) > http://biomolecularnmr.ihsr.dom/ > ------------------------------- > > ******************************************************************** > Sostieni la ricerca del San Raffaele con il 5permille! > E' SEMPLICE E NON COSTA NULLA. > Basta indicare nell'apposito riquadro della dichiarazione dei > redditi ("Ricerca sanitaria") > il codice fiscale della > Fondazione Centro S. Raffaele del Monte Tabor: > 03 06 42 80 153 e ricordarsi di firmare. > Se vuoi saperne di piu' scrivi a 5permille(~)hsr.it o vai sul sito > www.5xmille.org> > > > ------=_Part_100947_24436336.1180025818752 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear andrea,
 
Thank you for your response, now I could install haddock i.e i could source it successfully, not only haddock, but CNS and python but what i didn't understand is
1. what is the significance of ARIA, should we install ARIA to run haddock. 
2. i learn that run.CNS is the file where we have make the changes to run haddock and should execute that file, but where should we execute it, is it in python, CNS or haddock directories....
3. in this process of installation i didn't give the path of python, where should we give that.
 
and also i apologise for my delay in gratitude for ur response.
 
Thank you in advance,
 
P.Kalyan
 

On 5/22/07, andrea spitaleri spitaleri.andrea%a%hsr.it <owner-chemistry],[ccl.net> wrote:

Sent to CCL by: andrea spitaleri [spitaleri.andrea_._hsr.it]
Hi,
I am actually using HADDOCK and  it quite easy to install it:
1. install python & cns
2. copy somewhere the haddock package
3. set the environment
that's it!
for more information, just have look to the HADDOCK mailing list

Regards

andrea

Kalyan chaitanya kalyanpulipaka###gmail.com wrote:
> Dear all,
>
> Is there any one who have worked with HADDOCK for protein-protein
> docking, iam facing a challenge with installation of the same software....
>
> Thanks in advance,
>
> P.Kalyan.

--
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
-------------------------------

********************************************************************
Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Ricerca sanitaria")
il codice fiscale della
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a 5permille(~)hsr.it o vai sul sito
www.5xmille.org



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