From VSCHELDE@STEEVAST.RUG.AC.BE Mon Sep 14 05:12:07 1992 Date: Mon, 14 Sep 92 10:21 N From: VSCHELDE%STEEVAST.RUG.AC.BE@OHSTVMA.ACS.OHIO-STATE.EDU Subject: Proteins in solvent model To: CHEMISTRY@ccl.net Hi everybody , As a beginning researcher I am looking for force fields to model proteins in water. Is it possible to send me information on that matter. Or where can I get good programs to model proteins in water? I would be very greatfull if you could help me. Verschelde Jean-Luc Lab. for Mathematical and Computational Physics,RUG Krijgslaan 281 S9 9000 Gent,Belgium From martin@mg.sunet.se Mon Sep 14 15:18:47 1992 Date: Mon, 14 Sep 92 13:18:47 +0200 From: martin@mg.sunet.se (Martin Norin, Dept. Biochem., Royal Inst. Technol., Stockholm, tel. +46-8-7907512, e-mail; martin@physchem.kth.se) To: "chemistry@ccl.net"@kth.sunet.se Subject: MD simulations in apolar solvents... Dear Colleagues, Consider a protein in a hydrophobic environment (Crambin in an apolar solvent or a lipase in a lipid layer). You run two MD simulations with two boundary conditions. The first is vacuum and the other is explicit apolar solvent molecules and periodic boundary conditions. Will there be great differences in the trajectories and what differences ? Contradictory to simulations which mimics a protein in water I expect the vacuum boundary to be a much better approximation for the apolar solvent. I have seen studies where a Langevin algorithm succesfully replaced explicit apolar solvent molecules but no study as decsribed above. If anybody has studied this problem I would be very interrested in any references. I'll summarize the answers to anybody who is interrested or to the net if there a many inrterrested. Thanks, Martin Norin KTH Stockholm e-mail:martin@physchem.kth.se From coolidge@usafa.af.mil Mon Sep 14 01:54:32 1992 Date: Mon, 14 Sep 1992 07:54:32 -0600 From: "Michael B. Coolidge" To: B130778@vax.csc.cuhk.hk, CHEMISTRY@ccl.net Subject: Re: Does a Transition Structure (TS) have to connect 2 minimum? >Does a Transition Structure (TS) have to connect 2 minimum? For a paper that contains an example of one that does not, look in JACS for recent articles by Hrovat and Borden on cyclo-octa-tetraene. Michael Coolidge From cabku01@mailserv.zdv.uni-tuebingen.de Mon Sep 14 18:54:37 1992 Date: Mon, 14 Sep 92 16:54:37 +0200 From: cabku01@mailserv.zdv.uni-tuebingen.de (Hartwig Kuehbauch) To: chemistry@ccl.net Subject: RFD: sci.chem.organomet as a new newsgroup Dear netters! As most of you'll know there is a substantial lack of science newsgroups, especially related to chemistry. To my knowledge there are only the groups sci.chem sci.engr.chem Also there are some mailing-lists related to chemistry as, for example chminf-l chemistry orgche (seems to be NOT active) It's a pity that normally these lists and groups didn't support special parts of chemistry, such as organic-, inorganic- or physical-chemistry. Another major part of todays chemistry is held by organometallic chemistry. A subject which seems to be totally unknown to the net. Therefore I want to initiate the discussion about a new newsgroup called sci.chem.organomet This newsgroup could be a home for all chemists who work on organometallic chemistry, but also for all people who work on organic chemistry, because an organometallic chemist is always an organic chemist too! This newsgroup should be unmoderated. That's my opinion, but surely that's something to clear in this discussion. So please, all you chemists out there, help me in getting this newsgroup online! Regards Hartwig Kuehbauch ============================================================================= = Hartwig Kuehbauch - University of Tuebingen - Dep. of Inorg. Chemistry II = = (cabku01@mailserv.zdv.uni-tuebingen.de) - Germany - = ============================================================================= From theresa@si.fi.ameslab.gov Mon Sep 14 05:45:54 1992 From: theresa@si.fi.ameslab.gov (Theresa Windus) Subject: 2 TSs To: chemistry@ccl.net () Date: Mon, 14 Sep 92 10:45:54 CDT Hello! (again) Jorge Seminario has informed me that I wrote down the wrong reference for my own paper! The reference should be JACS, 113, 4356-4357 (1991). Hope this helps!! Theresa Windus Department of Chemistry Iowa State University Ames, IA 50011 e-mail: theresa@si.fi.ameslab.gov From jackels@hbar.phy.wfu.edu Mon Sep 14 10:03:39 1992 Date: Mon, 14 Sep 92 14:03:39 -0400 From: jackels@hbar.phy.wfu.edu (c.jackels) To: chemistry@ccl.net Subject: Sparc10 Benchmarks Does anyone know of any useful benchmarks for the Sun Sparc10, models 30 and 41? The only information I have come across is that which is furnished by Sun. Thankyou. Charles F. Jackels Department of Chemistry, Box 7486 Wake Forest University Winston-Salem, NC 27109 (919) 759-5511 FAX:(919)759-4656 Internet:jackels@hbar.phy.wfu.edu ~ From jk@biosym.com Mon Sep 14 14:38:06 1992 Date: Mon, 14 Sep 92 11:41:00 -0700 From: jk@biosym.com (Kottalam) To: chemistry@ccl.net Subject: Taking pictures from the screen Why, taking pictures from the screen is the easiest form of photography. The subject is not moving. You can overexpose to death to get maximum brightness. Since the picture is on a flat surface, you don't need to worry about depth of field. Since you will be using a tripod, film speed, and lens speed are not very important. But please, please don't use a flash; that would only wash out the picture on the screen, right? More important than the photography is the preparation of the picture on the screen. Use a dark background. Use bright colors to render the model. Adjust the brightness, line thickness and contrast in such a way that features are clearly visible from a distance. Turn out the room light if possible. Given these conditions, any film would faithfully reproduce the pictures. I use Kodachrome 64 if you must know. Compose the picture using a tripod at a convenient distance, say a little farther than the minimum focal distance of your lens. With a zoom lens, you have more flexibility on the tripod position. Make sure that all of the model is covered and all of the picture frame is filled. Choosing the aprerture: Since you don't need depth of field, you can use a large aperture (i.e., a small f-stop). But with large apertures, sharp focussing becomes critical and so you may want to close down a bit. Exposure time: Unfortunately, you cannot use the auto-exposure feature, no matter how sophisticated your camera is. This is because the light is not distributed uniformly on the screen. You may need to experiment. Use bracketing, i.e., shoot the same picture at different exposure levels and choose the best one after developing. I would try a quarter, half and a full second. Note that this is much slower than the scan rate on any monitor. These are long exposure times; your tripod and hand should be steady. A final word of wisdom: If your picture does not turn out well, you cannot blame me. Kottalam jk@biosym.com (619) 546 5366 \ | / Scientists are objective; - O - The Earth sucks and they call it gravity. / | \ From COGORDAN@unamvm1.dgsca.unam.mx Mon Sep 14 20:12:09 1992 Date: Mon, 14 Sep 92 16:51:24 MEX From: JUAN ANTONIO COGORDAN Subject: band structure To: CHEMISTRY@ccl.net Dear netters, We are interested in computing band structures of some compounds. Does anyone know where I can find public domain programs ? Thank's in advance. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ MAILING ADDRESS: JUAN ANTONIO COGORDAN INSTITUTO DE INVESTIGACIONES EN MATERIALES UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO APDO. POSTAL 70-360 07510 MEXICO D. F. MEXICO. ======================================================================== PHONE: (5) 622 4631 FAX: (5) 548 2703 BITNET: COGORDAN AT UNAMVM1 ========================================================================