From owner-chemistry@ccl.net Tue Dec 9 01:58:01 2008 From: "Kamalakar Jadhav kjadhav^^^vlifesciences.com" To: CCL Subject: CCL: Workshop on CADD and VLifeMDS training Message-Id: <-38264-081209015623-32055-CfGba+zublF6KORP5KUetg-$-server.ccl.net> X-Original-From: "Kamalakar Jadhav" Date: Tue, 9 Dec 2008 01:56:19 -0500 Sent to CCL by: "Kamalakar Jadhav" [kjadhav\a/vlifesciences.com] All India Workshop on Recent Advances in Computer Aided Drug Design to be convened at Bioinformatics Infrastructure Facility, University of Madras during December 17-20, 2008. The lectures on various topics on CADD will be delivered by the scientists from VLife and other prominent speakers from different institutions on 17th and 18th December 2008. A special hands-on session is planned on19th & 20th December 2008 covering all the modules of VLife MDSTM software. Contact on or before 17th December 2008 Prof. D. Velmurugan Co-ordinator Bioinformatics Infrastructure Facility (BIF) University of Madras Guindy Campus Chennai- 600 025 d_velu() yahoo.com velmurugandevadasan() gmail.com OR Amit Bedi VLife Sciences Technologies Pvt. Ltd amitb() vlifesciences.com regards Kamalakar From owner-chemistry@ccl.net Tue Dec 9 02:33:00 2008 From: "Kamalakar Jadhav kjadhav*vlifesciences.com" To: CCL Subject: CCL: Workshop on CADD and VLifeMDS training Message-Id: <-38265-081209020110-1437-lPUcNGyI31taDpz109UldA|-|server.ccl.net> X-Original-From: "Kamalakar Jadhav" Date: Tue, 9 Dec 2008 02:01:06 -0500 Sent to CCL by: "Kamalakar Jadhav" [kjadhav:vlifesciences.com] All India Workshop on Recent Advances in Computer Aided Drug Design to be convened at ioinformatics Infrastructure Facility, University of Madras during December 17-20, 2008. The lectures on various topics on CADD will be delivered by the scientists from VLife and other prominent speakers from different institutions on 17th and 18th December 2008. A special hands-on session is planned on19th & 20th December 2008 covering all the modules of VLife MDSTM software. Contact on or before 17th December 2008 Prof. D. Velmurugan Co-ordinator Bioinformatics Infrastructure Facility (BIF) University of Madras Guindy Campus Chennai- 600 025 d_velu- -yahoo.com velmurugandevadasan- -gmail.com OR Amit Bedi VLife Sciences Technologies Pvt. Ltd amitb- -vlifesciences.com From owner-chemistry@ccl.net Tue Dec 9 06:31:01 2008 From: "Vincent Vivien vincent[*]eyesopen.com" To: CCL Subject: CCL: Call for papers: OpenEye EuroCUP III - April 22-24, 09 - Toledo, Spain Message-Id: <-38266-081209062729-8931-i+vdKBcXXsk6baMBtw2oSg _ server.ccl.net> X-Original-From: "Vincent Vivien" Date: Tue, 9 Dec 2008 06:27:25 -0500 Sent to CCL by: "Vincent Vivien" [vincent===eyesopen.com] Dear Colleague, After Sheffield in 2007, and Strasbourg in 2008, OpenEye will hold its 3rd Annual European Molecular Modeling Meeting in the World Heritage city of Toledo, Spain, on April 22-24, 2009. We anticipate the four EuroCUP III Main Sessions to cover: * Shape and Electrostatics * QSAR: Is it Worth it? * Fragment Design: Good Idea or the Latest Blind Alley? * Databases and Data Sources for Molecular Modeling There are speaking slots available and also poster exhibitions. ** NOTE THAT YOU DO NOT NEED TO BE A CUSTOMER OF OPENEYE SOFTWARE TO PARTICIPATE! ** So if you would like to contribute or attend please follow the link below. http://www.eyesopen.com/forms/eurocup3_reg.html We are delighted that Professor Dr. Juergen Bajorath has agreed to give the Allocution entitled: "The role of journals in computational chemistry". In addition to the Main Sessions, we will hold a half-day Toolkit Session, where OpenEye toolkit users will have the opportunity to share some of their work. An OpenEye Training Workshop on Python/OEChem will also be available on April 21st for those interested in programming (limited to 10 trainees!). As always, except for the training, there is no registration cost for the meeting. Attendees need only cover travel and accommodation. We very much hope you will be able to join us in Toledo! With kind regards, Vincent Vivien Director of European Accounts OpenEye Scientific Software Office: +33 389 589 544 vincent[A]eyesopen.com ----------------------------------------------------------------- EuroCUP III details below. Also available from OpenEye website at ----------------------------------------------------------------- http://www.eyesopen.com/about/events/cup-eurocup/eurocup3-welcome.html -------- SCHEDULE -------- * Tue, April 21st (9:30am - 6pm): Training on Python/OEChem (10 trainees!) * Wed, April 22nd (9:30am - 1pm): Toolkit Session * Wed, April 22nd (3:00pm) to Fri, April 24th (12:30pm): Main Sessions --------- DEADLINES --------- * Abstract submission deadline for talks: February 13th, 2009. * Abstract submission deadline for posters: March 27th, 2009. * Registration deadline: April 10th, 2009. Because of the limited number of rooms available at the conference hotel however, it is likely that these will be filled well before that date. So please register early! ----- HOTEL ----- The location of the meeting and official hotel is the Parador Toledo. http://www.parador.es/en/cargarFichaParador.do?parador=079 You do NOT need to book the hotel yourself, OpenEye will make the reservation for you with the info you will provide in the registration form. ------ TRAVEL ------ Those flying will want to aim for Madrid Bajaras International Airport (MAD). OpenEye will organize a shuttle service from the airport directly to the conference hotel (about 1 hour's travel time). Please let us know about your arrival and departure time at MAD so that we can schedule the shuttle service to minimize waiting time. You may also use taxis and public transportation from MAD to Toledo, although it will require going through Madrid, which is not as convenient. ------------------ COSTS AND PAYMENTS ------------------ Except for the Python/OEChem training, the cost only covers delegates' accommodation, full board with wine tasting / conference dinner, and shuttle service to and from airport. * Python/OEChem Training (1 night / 1 day): 600 EUR (prepayment required!) * Toolkit Session (1 night / 0.5 day): 250 EUR * Main EuroCUP III Sessions (2 nights, 2 days): 550 EUR Payments covering the Toolkit session and Main EuroCUP III sessions will be made directly to the hotel upon checkout, together with any incidentals, unless prior arrangement has been made with EuroCUP organizers. Please see the registration form for details of what's included, as well as pricing options for local delegates. ----------------- STUDENT BURSARIES ----------------- A limited number of student bursaries are available for poster presentations. These will cover the costs associated with attendance to the Main EuroCUP III Sessions, i.e. the accommodation, full board and transportation to and from MAD airport using the shuttle service. For consideration, please use the registration form to submit your poster abstract and use the comments field to precise that you are applying for a student bursary. From owner-chemistry@ccl.net Tue Dec 9 10:21:01 2008 From: "Narasimhan Loganathan narasimhan.loganathan#etu.univ-provence.fr" To: CCL Subject: CCL: Rotating a molecule Message-Id: <-38267-081209045419-26370-MCMfOy9MFnnxximHOf+l7w\a/server.ccl.net> X-Original-From: "Narasimhan Loganathan" Date: Tue, 9 Dec 2008 04:54:14 -0500 Sent to CCL by: "Narasimhan Loganathan" [narasimhan.loganathan*_*etu.univ-provence.fr] Dear all, I have a molecule which has same energy for two different orientations. Now i am trying to study the energy of the molecule by rotating the molecule within those two orientations. But i am not aware of how to rotate a molecule. I tried this in molden using th XYZ coordinates but it didnt work. Can anyone help in this regard of how to rotate a molecule. Thanks in advance Naresh From owner-chemistry@ccl.net Tue Dec 9 10:55:00 2008 From: "Michael K. Gilson gilson()umbi.umd.edu" To: CCL Subject: CCL: translational entropy and solvation Message-Id: <-38268-081209104718-28081-4GjuFFEF5Zq4C2lBM6WZEg^server.ccl.net> X-Original-From: "Michael K. Gilson" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 09 Dec 2008 10:46:48 -0500 MIME-Version: 1.0 Sent to CCL by: "Michael K. Gilson" [gilson__umbi.umd.edu] Dear Raphael, I disagree: it is not obvious that the translational entropy changes on going from ideal gas to solution, because there is a clear-cut definition of translational entropy, as laid out in my prior posting, which does not change during solvation, if the molecule has the same accessible volume in the gas and solution phases. With classical stat thermo, at least, there's a straightforward way of looking at it, as follows. In gas phase, the partition function of a molecule in a box of volume V is proportional to V, and the volume term gives the translational entropy. It's something like -Rln V. In solution phase, the molecular partition function is still proportional to volume, so the translational entropy will be the same as it was in the gas phase if the volume of the system is the same. This can be seen if you imagine placing the solute anywhere in the solvent-filled box and initially computing the part of the partition function that comes from integrating over only solvent degrees of freedom. This integral is independent of where you placed the solute, so one can then complete the partition function by integrating over the volume of the solvent-filled box to get a factor of V. Thus, there is a factor of V in the molecular partition functions for the molecule in both gas-phase and solution, so the translational entropy is the same in both environments. By the way, it is the integral over the solvent degrees of freedom, mentioned above, that gives the solvation free energy which an implicit or explicit solvation model tries to capture. As a final note, I left out rotational entropy, but it follows a pattern just like the translational Regards, Mike From owner-chemistry@ccl.net Tue Dec 9 13:48:00 2008 From: "Purisima, Enrico Enrico.Purisima|cnrc-nrc.gc.ca" To: CCL Subject: CCL: translational entropy and solvation Message-Id: <-38269-081209131147-21667-uKxuO21mT4w7naKs8bEBYw+/-server.ccl.net> X-Original-From: "Purisima, Enrico" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 9 Dec 2008 12:39:18 -0500 MIME-Version: 1.0 Sent to CCL by: "Purisima, Enrico" [Enrico.Purisima[-]cnrc-nrc.gc.ca] Just to follow up on Mike Gilson's post, it is important not to confuse the translational mobility of a molecule with its translational freedom. In solution, it takes longer compared to the gas state for a molecule to get from point A to point B due to all the collisions but this does not in any way restrict the freedom of the molecule to be at point A or point B. Hence, being in solution does not reduce the number of translational states that a molecule has available to it, which is what matters for entropy. It's how many states there are and not how long it takes to sample those states that's relevant. Enrico From owner-chemistry@ccl.net Tue Dec 9 17:22:01 2008 From: "Raphael Ribeiro raphaelri{=}hotmail.com" To: CCL Subject: CCL: translational entropy and solvation Message-Id: <-38270-081209171918-16257-JSIENBhnwSwxnF88kg2VOQ*|*server.ccl.net> X-Original-From: "Raphael Ribeiro" Date: Tue, 9 Dec 2008 17:19:14 -0500 Sent to CCL by: "Raphael Ribeiro" [raphaelri a hotmail.com] Dear Michael, I think you forgot that the mathematical expression that you're talking about for translational entropy is based on the ideal gas model, the partition function in this case is calculated using the particle in a box model.In this case the problem of calculating the energy levels of the whole system is reduced to calculating the energy levels of a molecule (translational,rotational and vibrational energy levels of the molecule). Also,and more important, as you might know in this formulation no intermolecular forces or external fields are considered. If you look at Landau and Lifschitz, Vol.5 Statistical Physics, you are going to see that when he talks about the ideal Boltzman gas(pages 120-123) he derives the equation of state of an ideal gas using a partition function that was calculated using the translational energy levels we're talking about (particle-in-a-box energy levels) and also the energy levels of the internal motion of the ideal gas. This means that systems in which the translational partition function is calculated by the particle-in-a-box model have the equation of state of an ideal gas. That is why I can not agree that translational partition functions are the same in the ideal gas phase and in the solvated phase. Again, http://biophysics.med.jhmi.edu/amzel/people/siebert/strsl_2col_bw_letter.pdf in this article the authors talk about a statistical mechanics framework for the estimation of translational entropy loss in associations while taking explicitely into account the intermolecular interactions between the solute and the solvent, it is called CM formalism. The following quote from the paper corroborates what I said before about ideal gas translational partition function and non-ideal gas translational partition function, by talking about the entropy in different systems (entropy and partition functions are directly related). "Thus, the estimation of dStrans depend solely on the evaluation of the integral in Eq.2 which, after integration over the momenta dp, yields: Eq. 4 where (De Broglie wavelenght) = h/(2piMkT)^1/2 is the de Broglie wavelength of a solute molecule. If the N solutes were an ideal gas (i.e. without solvent nor intermolecular interactions, (U=0), the integral in eq. 4 would be equal to V, leading to the so called "Sackur-Tetrode"(ST) formula for translational entropy[14]: Eq.5 This formula is sometimes used as the basis for estimating entropies of molecular associations in solution[3,13,16]. However, the presence of a nonzero potential U complicates considerably the evaluation of the configurational integral in Eq.4, requiring approximate methods[1]. The goal of this paper is to provide a framework based on cell models [2,15,17,18], to approximate efficiently dStrans." As you might have noticed the presence of an external potential (create by intermolecular forces) changes the way(ideal gas phase model) we calculate translational entropies. And that is why people make models to calculate this component of entropy (as it was done in this paper) and understand the role of translational component of entropy in some situations. This other article http://www.biophysj.org/cgi/content/abstract/89/4/2701 uses a sophisticated statistical mechanic theory to analyse the role of translational entropy of solvent molecules in the proteing folding process. To conclude, the molecular partition function we've learned and are used to work with is very good for ideal gases system, but not for solvated systems, as it does not include molecular interactions and without interactions there would be no solvated phase. Raphael Ribeiro