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EMERSON CENTER Newsletter A Publication of the Cherry L. Emerson Center for Scientific Computation, Emory University http://www.emerson.emory.edu Volume 8, September 15, 2001 COMPUTATIONAL CHEMIST JAMES KINDT Inside This Issue . JOINS EMERSON CENTER ✾ New Professor & User to EC (p. 1) ✾ The Emerson Center welcomes Dr. James Kindt, who has recently joined the Department New EC Equipment Purchase of Chemistry as an Assistant Professor and a new subscriber to the Emerson Center. His (p. 1) office and laboratory are located in the Emerson ✾ Emerson Center Fee Change (p. 1) Center on the 5th floor of the Cherry Logan ✾ ECEC Meeting Minutes (p. 1) Emerson Hall. Prof. Kindt’s specialty is ✾ computational chemistry, in particular, modeling EC Visiting Fellowship Announce- of biomolecular systems. He says that his primary ment & Letters from Fellows (p. 2) research goal will be to explore, by computer ✾ Research Reports from Emerson simulation and theory, how lipid composition and Ctr. (p. 3) molecular structure contribute to the organization ✾ Technical Specs on EC Hardware and structure of lipid bilayers. He will be using (p. 4) Emerson Center’s computational and graphic ✾ facilities extensively for his research. He recently Emerson Center Contact Info received a prestigious New Faculty Award from (p. 4) the Camille and Henry Dreyfus Foundation. Prof. Professor James T. Kindt Kindt received his PhD from Yale University and was a postdoctoral fellow at UCLA before joining Emory. Please refer to page 3 of this newsletter for one of Prof. Kindt’s research proposals using the Emerson Center facilities. New Biomolecular Modeling & Visualization Facility at EC In the News In response to popular demand from the biomolecular modeling community at Emory and with grant support from the National Science Foundation, the Emerson Center ◆ Emerson Center Fee recently established its new Biomolecular Modeling and Visualization Facility. This facility Change consists of one SGI Origin3200 as a compute server and two SGI Octane2 graphics With approval from the Em- workstations (with 2 processors each) for visualization and computing. The new facility erson Center Executive Com- supports a variety of biomolecular modeling software, mittee, the Emerson Center including MacroModel, Sybyl, Cerius2, Amber and subscriber fee is increased by Tinker, some of which are available only on the SGI 5% effective September 2001. platform. The superb graphics engines will provide The new fee will be $1312.50 image processing and opportunities for many other for one unit and $5250 for applications. Technical details of the facility are one share. This is the first fee reported on page 4 of this newsletter. This facility increase since the center’s supplements the capability of the High Performance subscriber program started Computing Facility at Emerson Center, which was in 1992. This increase is nec- essary to meet the needs for acquired in December 2000 and consists of an IBM increased costs in hardware SP supercomputer complex with 58 Winterhawk II CPUs. Anyone interested in trying and software maintenance out our new Biomolecular Modeling and Visualization Facility as well as the High and in the increasing person- Performance Computing Facility is encouraged to contact the Emerson Center. nel expenses. For details re- garding the Emerson Center fee schedule and related sub- NEWS FROM THE ECEC MEETING scriber benefits, please refer The Emerson Center Executive Committee (ECEC) met on Thursday, Sept. 13, 2001, to the Emerson Center webpage at http:// to discuss issues related to the new school year. On the agenda were administrative www.emerson.emory.edu/ issues including membership, income & expenses, and the EC newsletter. A detailed technical report was presented by the center’s scientific staff about the new SGI com- Cover/EC_Fee.html. puter and related software purchase. Plans for 2001-2002 were discussed including budget issues, the Visiting Fellows Program, technical staff salaries and additional hardware upgrade of the center’s equipment. A 5% increase to the subscriber fee was approved by the committee. Please refer to “In the News” section on this page for details about the increase. Letters from Fellows EMERSON CENTER VISITING FELLOWSHIP When I arrived to Emory in July of 2001 for a one-month stay I was certainly not a The Emerson Center offers visiting fellowships to interested scientists through- newcomer, neither to this Center nor to this out the year. Scientists from academic institutions all over the world who want fellowship. However, I was gladly surprised by to perform intensive research in computational chemistry, physics, and other the quality of the new installations in the recently sciences for one to several months are encouraged to apply. We also accept built Emerson Hall, and by the substantial increase faculty on sabbatical leave. Postdoctoral research associates are not supported in computer power. This has made the stay even through this program. Travel expenses (and stipends for long term stays) are more pleasant and fruitful than previous ones, and available. Although fully independent research is not excluded, collaboration this was certainly a demanding goal. Another with an EC subscriber is desirable, and EC subscribers are encouraged to substantial factor contributing to the fruitful visit has been the continued hospitality from Prof. make recommendations. The deadline for Emerson Center Visiting Fellowship Morokuma and Dr. Musaev. Ms Jianli Zhao has applications for summer 2002-summer 2003 is February 1, 2002. To formally also been extremely helpful in solving the small apply, please submit: administrative problems in which foreign visitors • 1-2 page research proposal (or at least me) have • CV including publication list a certain ability to • Amount of financial support needed run into. • Length of stay with an approximate start/end date The scientific Applications should be submitted to the Emerson Center (address on p. 4). work during this stay focused on an APPLICATION DEADLINE: FEBRUARY 1, 2002 analysis of the performance of quantum mechanics/ molecular mechanics My Stay at the Emerson Center as a Visiting Fellow (QM/MM) methods Dr. Ilkay Oren, Associate Professor, University of Ankara, Turkey in the reproduction I would like to thank the Emerson Center for giving me the opportunity to work of steric interactions. with Professors Dennis Liotta and James P. Snyder. I joined the Liotta-Snyder group Dr. Feliu Maseras I had the chance to on November 1, 2000. My stay at the Emerson Center has been incredibly pleasant contribute to the and most educational in many ways. It is particularly exciting to be able to study original development of one of these methods with the excellent teaching, patience and guidance of Professor Jim Snyder. (IMOMM) during a previous stay. This scheme has proven to be very efficient for the introduction When I came here I knew very little about computational chemistry. During my of bulky ligands in the accurate modeling of real first three months, I focused on learning how to communicate with the computer transition metal complexes. However, as the network loaded with Macs and PC’s, Silicon Graphics workstations and IBM mini- applications of the method keep growing, it supercomputers. I was also introduced to several sophisticated pieces of software. becomes critical to obtain a better understanding For example, it was a delight to use the MacroModel force field engine, build of its strengths and weaknesses. The goal of this structures, optimize their geometries visit consisted of evaluating the performance of and carry out conformational different theoretical treatments on the analyses. Following that, I became reproduction of the steric interactions, which is engaged in a project devoted to part the main feature of the IMOMM method. Several of the biosynthetic pathway of the small model systems presenting the closed shell/ antitumor agent, Taxol. I had closed shell interaction characteristic of steric previously dreamed of working in this effects have been chosen, and submitted to area, but was unsure whether the calculations with a large variety of computational opportunity would ever present itself. methods, including several force fields and high Molecular Mechanics is insufficient level quantum chemical methods. The current to understand the pathway involving results, which are still not final, suggest that MM carbocationic intermediates. methods reproduce better the steric interactions Therefore I had to learn how to use than some of the lower range of QM methods, Quantum Chemical Methods. Ab including Hartree-Fock. This has the interesting initio and density functional theory consequence that, in some particular cases, a QM/ Dr. Oren and Dr. & Mrs. Cherry L. Emerson at (DFT) calculations with Gaussion-98 the Emerson Center Open House in April 2001 MM calculation can be more accurate than a full (at the Emerson Center) are both more QM calculation on the same system. appropriate and more accurate. While I was working on this project, I also started to After this brief report of my research, I want focus on NMDA antagonists. These compounds are a potential remedy for the to use the last paragraph of this letter to thank the completely untreatable condition of stroke. During this second project I have learned Emerson Center Visiting Fellowship program for how to search for pharmacophores using APOLLO. Now, I intend to apply PrGen to giving me the chance to visit this great center, create a pseudoreceptor for the NMDA ligands. It will be so exciting… and to inform all the readers of this Newsletter In addition, I have enjoyed very much having so many members of the Liotta- what a great opportunity these fellowships Snyder group around to talk with and share a game of badminton and volleyball. It constitute to do research. has also been a pleasure to drink an evening coffee with Prof. Snyder and having *Dr. Maseras is Associate Professor of Chemistry at lunch once a month with Emerson Center staff and other Fellows.
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