From chemistry-request@server.ccl.net Fri Dec 7 20:22:07 2001 Received: from rwcrmhc53.attbi.com ([204.127.198.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB81M6i22411 for ; Fri, 7 Dec 2001 20:22:07 -0500 Received: from rwcrwbc56 ([204.127.198.45]) by rwcrmhc53.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with SMTP id <20011208012149.IWTH24045.rwcrmhc53.attbi.com@rwcrwbc56> for ; Sat, 8 Dec 2001 01:21:49 +0000 Received: from [12.226.196.89] by rwcrwbc56; Sat, 08 Dec 2001 01:21:48 +0000 From: greenops@attbi.com To: chemistry@ccl.net Subject: The Completed Paper on Comp Chem Career Date: Sat, 08 Dec 2001 01:21:48 +0000 X-Mailer: AT&T Message Center Version 1 (Nov 29 2001) Message-Id: <20011208012149.IWTH24045.rwcrmhc53.attbi.com@rwcrwbc56> Dear CCL-ers, First of all, I would like to say thank you to all who answered my survey about computational chemistry. It went very well and I had a lot of good answers. Second, I would like to apologize to everyone who tried to email me recently and got an 'undeliverable' message. I was one of the unlucky people with @home, and so when the company went bankrupt, I lost internet for a while. Last of all, I am including my paper for all those interested. Regretfully, I have to say that some of your answers have made me begin to rethink my career choice, but the survey was still very informational, I am glad I did it, and thanks again for all your help. Best wishes, Linda M. Prengman Ringgold High School 124 Briarwood Dr. 1 Ram Drive Monongahela, PA 15063 Monongahela, PA 15063 ========================================================================= Linda Prengaman Miss Ciccone Period 3 December 5, 2001 Computational Chemistry What is computational chemistry? Dr. Allen Richon, Ph.D., writes that, "Not very many people know about it, even chemists." (Richon). The Encyclopedia of Computational Chemistry gives the following explanation: Computer methods are used to solve any mathematical problems concerning chemistry, physics, etc, which would be nearly impossible using experimental methods. In it's short thirty-year history, computational chemistry has proven itself worthy of being acknowledged as a subdivision of chemistry. This discipline has applications that can be applied to all areas of chemistry and has impacted the work of all chemists, significantly increasing efficiency in a number of fields (Encyclopedia). Dr. Lisa M. Balbes, Ph.D. sums up her job this way, "I am a chemist, and I use the computer to help design new drugs." (Balbes). Computational chemistry used to sound like a good idea to me because I love chemistry and computer programming. I did not really know too much about it, but I wanted to find out more. Obviously, I need to know something about how to get from here to there. The first important step is getting the proper education. Not many colleges offer computational chemistry as a major because it is an incredibly rare one, and not many people know what it is. One of the very few colleges that offer it is Carnegie Mellon University. Once in college, I will be spending quite a few years there. According to Dr. Allen Richon, a computational chemist, I will need to get a BS in Chemistry, a Ph.D. in Computational Chemistry, and then do at least two years of post-doctoral research. Most likely I will finally get a job around age 27 (Richon). Sudhakar Pamidighantam tells me that I will need to have a strong background in general chemistry, mathematics, and computational sciences (Pamidighantam). Although there are some chemical societies who would like to see one implemented, at this time there is no special licensing requirement for computational chemists (Richon). Once I finish my post-doctoral research, there is nothing standing in my way of becoming a computational chemist. Suppose I am out of college, trying to get a job as a computational chemist. I need to worry about what kind of place will hire me, how easy it is to find a job, and whether my position will be secure. First, I have two main choices to make. I can either get a job working for an industrial company or doing hard research for a university. Research and development divisions of industries involved in materials, drugs and pharmaceuticals, and chemicals mainly usually employ industrial computational chemists and chemical software industry as well (Pamidighantam). In a survey I sent out to all computational chemists who subscribe to the Computational Chemistry List, most agreed that the future of computational chemistry is fairly secure because it is quickly becoming a very useful tool in chemistry. However, they also agree that it will always only be as essential as experimental chemistry, that it is not much good on its own (Prengaman). The availability of jobs is an interesting situation. Jobs are not offered everywhere because the profession is so rare. As one computational chemist that took my survey told me, "You have to go where the jobs are." (Prengaman). This does not mean that jobs are hard to find. While the job market is sparsely spread out all over the world, there are not enough computational chemists to fill the positions (Richon). Getting a job seems to be both easy and hard at the same time. Now I have a job offer. Before I accept it, I need to know what kinds of things I'll be doing, what my hours are, and how much money I'll make. Most of the computational chemists I surveyed told me that they spent most of their time reading chemistry journals and researching the work of their peers. Other things that they do include studying molecular models on the computer, running computer programs that allow them to do the actual computations, writing reports of their findings, talking to lab chemists about the theoretical results compared to what actually happened when the experiment was done in the lab, attending meetings with other research teams, and a lot more (Prengaman). The majority of the chemists told me that they spent very little time writing programs, and most of the programs that they did write were for their own private use. All of them reported long workdays, usually 10-14 hours, although the actual hours that they gave me varied. One interesting consistency in their answers was that many of them begin work later than typical in the morning and end late in the evening. For example, one computational chemist told me he worked from 10 AM to 7 PM. Another told me, "Being a computational chemist is, for me, 24x365 because the computers never sleep," and many reported that they did a good deal of work-related reading at home (Prengaman). The general feedback about salary was interesting. On the survey, the most popular answer to, "How much do they pay you?" was, "Not nearly enough." Dr. Richon told me that I would probably start out at about $80,000 per year, and that I could work my way up to making $125,000 per year (Richon). That corresponded well with the Chemistry Occupational Possibilities web site, which reported that most people in the chemistry field make $75,000-$100,000 per year (Chemistry). I began to wonder if the stress of the job is so high that it is not worth a salary close to or maybe even about $100,000 per year. Maybe this job is not such a good idea after all. In fact, by this time, I had begun to wonder about a lot of things. I had been told that I need to have a strong background in mathematics to excel in my potential profession. Quiet frankly, I do not do well in my math classes; therefore I do not like it, and I can think of few things worse than dealing with huge computations everyday at work. Also, tedious research bores me. I could not spend many hours per day reading chemical journals. Another thing that bothered me was that I might not spend much time writing programs, and this one was one the main reasons computational chemistry appealed to me before I knew much about it. The more I thought about it, the more I decided that computational chemistry might not be right for me. Works Cited: Balbes, Lisa M. "Re: Career in Computational Chemistry." E-mail to Linda Prengaman. 4 November 2001. "Chemistry Careers." Chemistry Occupational Possibilities. 20 November 2001. Encyclopedia of Computational Chemistry. . 7 Novemver 2001. Pamidighantam, Sudhakar. "Re: Career in Computational Chemistry." E-mail to Linda Prengaman. 12 November 2001. Prengaman, Linda. Personal Survey of Computational Chemists. 6 November 2001- 21 November 2001. Richon, Allen. "Re: Career in Computational Chemistry." E-mail to Linda Prengaman. 14 November 2001. From chemistry-request@server.ccl.net Sat Dec 8 09:39:21 2001 Received: from mh1-munich.munich.accelrys.com ([192.190.183.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB8EdLi17068 for ; Sat, 8 Dec 2001 09:39:21 -0500 Received: from dhcp48.munich.accelrys.com ([172.29.65.48] helo=accelrys.com) by mh1-munich.munich.accelrys.com with esmtp (Exim 3.12 #1 (Debian)) id 16Cid2-0004ov-00; Sat, 08 Dec 2001 15:39:00 +0100 Message-ID: <3C122604.5A40DF2@accelrys.com> Date: Sat, 08 Dec 2001 15:39:00 +0100 From: Christoph Schneider Reply-To: christoph@accelrys.com Organization: Accelrys X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: "nepenthes@vplaces.net" , "chemistry@ccl.net" , Ibrahim Moustafa Subject: Re: CCL:calculate/visualize electrostatic changes for protein-ligand References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Rowyna K., as you have been already told by Ibrahim, the forcefields today don't do that. But there are polarizable forcefields in developement which could be used for that purpose. So what you can do with Insight for example is to calculate the electrostatic potential (ESP) of the complex minus the ESP of the single molecules. That will give you an estimation of the binding energy of the complex. And since you can map the electrostatic potential on the surface, you can visualize the changes in the ESP as well. There are programs available that use the ESP to assign the partial charges, but I wouldn't do that for macromolecules, where a lot of atoms are buried in the interior of the molecule. regards C. -- ----------------------------------------------------------------------- Christoph Schneider PhD | Accelrys Inc. | christoph@accelrys.com Application Scientist | Inselkammerstrasse 1 | Tel: +49 89 61459 3 Life Science Group | D-82008 Unterhaching | Fax: +49 89 61459 400 ----------------------------------------------------------------------- From chemistry-request@server.ccl.net Sat Dec 8 12:49:22 2001 Received: from mail7.wlv.netzero.net ([209.247.163.57]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fB8HnLi20661 for ; Sat, 8 Dec 2001 12:49:21 -0500 Received: (qmail 14861 invoked from network); 8 Dec 2001 17:49:08 -0000 Received: from ppp-65-91-28-89.mclass.broadwing.net (HELO valued-customer) (65.91.28.89) by mail7.wlv.netzero.net with SMTP; 8 Dec 2001 17:49:08 -0000 Message-Id: <3.0.1.32.20011208125732.00822860@pop.netzero.com> X-Sender: zavialov@pop.netzero.com X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Sat, 08 Dec 2001 12:57:32 -0800 To: chemistry@ccl.net From: Ilia Zavialov Subject: Zero-point correction in Spartan Pro Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear collegues, I would like to find out if there is a way to calculate zero-point energy and thermal corrections to the total energy in Spartan Pro for Windows. Thank you very much for your help, Sincerely, Ilia A. Zavialov, Ph.D. zavialov@netzero.net ************************************************************ Sincerely, Ilia and Marina Zavialov zavialov@netzero.net marishazav@yahoo.com ************************************************************ maril95@hotmail.com ---------------------------------------------------- Sign Up for NetZero Platinum Today Only $9.95 per month! http://my.netzero.net/s/signup?r=platinum&refcd=PT97 From chemistry-request@server.ccl.net Sat Dec 8 10:22:30 2001 Received: from oxygen.chem.nthu.edu.tw ([140.114.45.223]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fB8FMTi18070 for ; Sat, 8 Dec 2001 10:22:29 -0500 Received: by oxygen.chem.nthu.edu.tw (Postfix, from userid 212) id 272EE15425; Sat, 8 Dec 2001 23:22:15 +0800 (CST) Date: Sat, 8 Dec 2001 23:22:15 +0800 From: chem@oxygen.chem.nthu.edu.tw To: chemistry@ccl.net Subject: Re: CCL:Gaussian 98 benchmark for PC systems Message-ID: <20011208232215.A10603@OXYGEN.chem.nthu.edu.tw> References: <20011206011124.A19953@OXYGEN.chem.nthu.edu.tw> <20011207230502.A23543@OXYGEN.chem.nthu.edu.tw> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <20011207230502.A23543@OXYGEN.chem.nthu.edu.tw>; from chem@oxygen.chem.nthu.edu.tw on Fri, Dec 07, 2001 at 11:05:02PM +0800 Dear Listers, We have got the information from Gaussian Inc. that distributing the modified version of makefile or the instructions is violation to the licence agreement. Sincerely, -- Yu, Jen-Shiang Kenny // jsyu@Platinum.chem.nthu.edu.tw http://oxygen.chem.nthu.edu.tw/~jsyu Theoretical Chemistry Lab, Department of Chemistry, National Tsing Hua University Hsinchu 300, TAIWAN