From ANIL@tifrvax.bitnet Thu Feb 27 06:06:51 1992 Date: Thu, 27 Feb 92 16:37 IST From: ANIL%TIFRVAX.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Subject: Regarding the Protein data bank To: chemistry-request Status: R i:, I am Dr. R.P. Ojha here. I have recently purchased the amber4. I am trying to install it on Iris 4D/70G. I am interested in the conformational studies of peptides. Molecular dynamics studies with amber require the protein data bank. which is not available in the amber package and in our library. Therefore, it will be difficult to start any computation in its absence. I would very much appreciate if you can arrange to send the protein data bank in my account through the e-mail. Further, I wish to join the e-mail reflector for the informations in the protein modelling. Please include my name among one of the users and oblige. Thanking you, Ojha From chemistry-request@ccl.net Thu Feb 27 08:36:29 1992 Date: Thu, 27 Feb 92 13:40:57 +0100 From: martin@link.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: Protein Databank. Status: R In responce to Dr. Ohja's request I can recommend the EMBL mail server for Brookhaven files on line. It contains a lot of other stuff as Swissprot databank, Enzyme databank, software etc, etc. Very useful. Just a mail containing the single line HELP , without typing in anything in the subject line, to NETSERV@EMBL-Heidelberg.DE and you'll get detailed information. Regards email: martin@physchem.kth.se /Martin Norin Dept. Biochem. KTH Stockholm From chemistry-request@ccl.net Thu Feb 27 08:36:50 1992 Date: Thu, 27 Feb 92 09:14:52 GMT From: "Steven S.B. Glover" Subject: Search for Information. To: CHEMISTRY@ccl.net Status: R I am currently in the middle of changing from a position involving primarily molecular mechanics and related calculations on small molecules (saccharides) to one where I will be working with protein and (to an extent) nucleic acid sequence information and structure. I would be very grateful for any information that members of this list could provide me with in the following areas: 1) Databases. Which databases of sequence and structure information exist? How can I get them? Are they available on tape, or must they be downloaded over the internet? If the former, what sort of costs are payable by an academic site, an academic site with commercial links, or a "full" commercial site? What size are the various databases, and what is the position on merging information between several of them? 2) Software. Which packages exist for analysis and exploration of the databases? How much is available "over the net", and what is sold commercially? Again, what are the costs for a straight academic site, an academic site with commercial links or a full commercial site? 3) Hardware. What machines do these programs need to run on? What is the minimum size of system that is normally used, and does it have serious limitations? In other words, is the minimum system normally used one that will JUST do the job, or is it a system that happens to have been already in existence and to which the software can easily be ported? 4) Other Considerations. Is there a parallel mailing list to this one for molecular biology? Can anyone recommend a good review of the field? As you can imagine, I'm rather "in at the deep end" with these questions, but I assumed that the Combined Wisdom of the Net ought to be able to give me a good idea of the information I need for this project. Thank you all very much, Steve Glover BPH6SSG@uk.ac.leeds.cms1 (british order) BPH6SSG@cms1.leeds.ac.uk (rest of world) PS it goes without saying that I will summarise and repost... From chemistry-request@ccl.net Thu Feb 27 15:27:55 1992 Date: Thu, 27 Feb 92 14:10:41 EST From: Dongchul Lim Subject: Re: coformational analysis in molecules (polymers) To: chemistry@ccl.net Status: R I found this article in sci.physics news group. I'm cross-posting it because it is likely to be better answered in this mailing list. -dongchul lim MALLON@rzmain.rz.uni-ulm.de (Mallon Rainer): > There are several approaches to do a convolutional analysis of molecules. > > 1.) Purely quantummechanical methods, the socalled ab-initio-methods. > > 2.) Semiempirical quantum - mechanical methods (like MINDO, MNDO, AM1 or > PCILO) where assuptions are made concerning the hamiltonian operator > and the wavefunction of the problem. > > 3.) Force - field - approaches where only interactions between two particles > are taken into account. (like the central - force - field or the > Urey - Bradley - force field.) > > My questions concerning these methods are : > > - Do You know an article where thes methods are compared to each other, > showing the different ways the work and the different results that can > be achieved ? > > - What purely quantummechanical methods are known ? Did anyone compute > more than lets says 100 atoms per molecule ? > > - Is there someone working with the PCILO method ? I would be glad to hear so. > > If i omitted an approach or a group of approaches, please tell me. > > Thanks in advance. > > Yours > RaMa. > > ------------------------------------------------------------------------------ > Rainer Mallon - University of Ulm - Germany - Department of Applied Physics