From chemistry-request@ccl.net Thu May 14 10:10:25 1992 Date: Thu, 14 MAY 92 11:40:53 GMT From: PARSONS_A@snd01.pcr.co.UK Subject: 2-D and 3-D NMR To: CHEMISTRY <CHEMISTRY@ccl.net> Status: RO Subj: 2-D and 3-D Protein NMR Greetings Networking Colleagues, This is not strictly a posting that may have DIRECT relevance to your group but I was wondering if there were any members of this group there who could point me in the right direction for BB's, SIG's, Discussion Groups, Software Fora, LISTSERVERS or COMSERVERS relating to the field of 2-D and 3-D NMR spectroscopy with particular reference to protein structure prediction. I do not subscribe to all the groups I am posting to so if you could mail me direct I would very much appreciate it and then I will post summaries back to the groups that express an interest. Many thanks, Tony Parsons Groups Contacted ================ iveuncc.bitnet::hiris-l ! High Resolution IR Spectroscopy umdd.umd.edu::ics-l ! International Chemometrics Society taunivm.tau.ac.il::interf-l ! Israeli Group on Interfacial Phenomena usachvm1.bitnet::mossba-l ! Mossbauer Spectroscopy, Software & Forum frors12.bitnet::share-l ! Spectroscopic Happenings on Actinides rpiecs.bitnet::orgche-l ! Organic Chemistry e-conference taunivm.tau.ac.il::physics-l ! Physics Fourum brufmg.anmg.br::fisica-l ! Physics e-conference rutgers.edu::polymerp ! Polymer Physics Discussion frulm11.bitnet::rbmi ! Groupe de Reserche en Biologie Moleculaire ubvm.bitnet::emflds-l ! Electromagnetics in Medicine uk.ac.leicester-poly::pharmex ! Pharmacy Mail Exchange ccl.net::chemistry ! Computational Chemistry e-conference From chemistry-request@ccl.net Thu May 14 11:03:57 1992 Date: 14 May 92 12:00:56 GMT From: Siegfried.Schneider@CNVE.RRZE.uni-erlangen.de To: CHEMISTRY@ccl.net Status: RO Hello, I am looking for an efficient algorithm to calculate the matrix of second derivatives of a function f(p) depending on N-parameters. Especially I am looking for an iterative method, something like the Romberg algorithm for first derivatives. Thanks in advance, Peter Peter Gedeck Inst.f.Phys.Chem. 1 Egerlandstr. 3 8520 Erlangen Germany FAX 09131 - 858307 E-mail : PC1@cnve.rrze.uni-erlangen.dbp.de From chemistry-request@ccl.net Thu May 14 12:46:13 1992 Date: Thu, 14 May 1992 09:26 CST From: C1790@slvaxa.umsl.EDU Subject: THANKS To: CHEMISTRY@ccl.net Status: RO DEAR FRIENDS, THANKS TO THOSE KIND PEOPLE WHO REPLIED TO MY REQUEST FOR THE PHONE NUMBER OF ERICH WIMMER. I WONDER IF ERICH REALIZES HOW MANY PEOPLE KNOW HIS WHEREABOUTS? BILL WELSH IN ST. LOUIS (C1790@UMSLVAXA). From chemistry-request@ccl.net Thu May 14 21:41:43 1992 Date: Thu, 14 May 92 18:52:50 CDT From: heller@lisboa.ks.uiuc.EDU (Helmut Heller) Subject: SUMMARY: Phospholipid charges To: chem@lisboa.ks.uiuc.EDU Status: RO A couple of weeks ago I posted a question on good molecular dynamics parameters for the simulation of lipids. I got several interesting answers which i would like to share with you. Date: Thu, 2 Apr 92 10:19:29 CST From: erickson@k.scs.uiuc.edu (Jon Erickson) To: heller@lisboa.ks.uiuc.edu Subject: looking for headgroup charges for PC (phosphatidyl choline) Helmut, Have you seen the following papers by Pedersen et. al. ? J. Comp. Chem., 1990, 11, 1181 J. Comp. Chem., 1991, 12, 899 and 1125 I hope they may be of some help. ---------------------------------------------------------------- Date: Sat, 4 Apr 92 13:53 EST From: "TERRY R. STOUCH (609)252-5442" <STOUCH@dino.bms.com> Subject: Re: looking for headgroup charges for PC (phosphatidyl choline) To: heller@lisboa.ks.uiuc.edu X-Envelope-To: heller@lisboa.ks.uiuc.edu X-Vms-To: IN%"heller@lisboa.ks.uiuc.edu",STOUCH Hello: I have been doing simulations of dmpc and dmpe bilayers and monolayers for several years now. The parameters that I have tested most extensively I have published in Journal of Computational Chemistry, 1991, 12(8), 1033. Analysis of the charges will be in the June 1992 issue of that journal. These have served well in simulations of lipid crystals and for several nanoseconds of bilayer (with explicit water) and monolayer simulations, however, I think that there is room for improvement. We are also working on even more rigorous force fields and plan to publish those as soon as we have tested and characterized them. These will include the most widely found headgroups and linkages. ---------------------------------------------------------------- Date: Tue, 7 Apr 92 09:14:47 -0400 From: alex@tammy.harvard.edu (Alex Mackerell) To: heller@lisboa.ks.uiuc.edu Subject: Re: lipid parameters Cc: paraman@tammy.harvard.edu Helmut, Thank you for your interest in the lipid parameters. Following this message will be the Charmm22 topology and parameter files. At this point in time the parameterization is essentially complete, with tests being performed on larger systems, including crystals. Thus, as you use the parameters any comments as to problems etc. are appreciated. If further adjusments are made you will be informed. Finally, a manuscript is in preparation. At the appropriate time I will forward a copy to you. Good Luck. Alex MacKerell alex@tammy.harvard.edu ---------------------------------------------------------------- From: Pitner@bdrc.bd.com Subject: Re: looking for headgroup charges for PC To: <heller@lisboa.ks.uiuc.edu> Cc: <Pitner@bdrc.bd.com> Date: Thu, 30 Apr 92 09:43:00 EDT Encoding: 40 TEXT X-Mailer: Network Courier V2.1b Helmut: 1.The most recent issue of J. Comp. Chem. (vol 13, no. 3, April) has an article on PC charges on p. 318 by Schaumberger and Koehler who compare various charge derivation methods: Mulliken, CHELP, and natural population analysis. They prefer the latter method and indicate these will be used in GROMOS calculations with PC and PC antibodies. 2. Rao and Singh (J. AM. Chem. Soc., vol. 111, 3125-3133, 1989) present free energy of hydration and charge calculations of charged ammonium species using AMBER which may be relevant to your work. 3. Charifson, Hiskey, and Pedersen (J. Comp. Chem., vol11, p.1181, 1990) discuss derivation of AMBER parameters using CHELP for modeling of phospholipids in water, which appears to be very similar to what you are doing. I have been using the Gaussian / CHELP charge method basically as described in 2 and 3 above with an AMBER parameter set and have found it to give reasonable results in protein docking studies. ---------------------------------------------------------------- I would like to thank all those who responded to my original question. The answers were very helpful to me and I hope this little summary is of some value to you. Servus, Helmut (W9/DH0MAD) _________________________________________________ heller@lisboa.ks.uiuc.edu "Knowledge must be gathered and cannot be given" FAX: (217)244-1080 ZEN, one of BLAKES7 Phone: (217)244-6914, ------------------------------------------------- Helmut Heller, University of Illinois at Urbana-Champaign, Beckman Institute Theoretical Biophysics Group, Room 3143, MC 251 405 N. Mathews Ave., Urbana, IL 61801, U.S.A.