From eldbjorg@chem.uit.no Sat Aug 17 08:18:04 1996 Received: from kvikk.uit.no for eldbjorg@chem.uit.no by www.ccl.net (8.7.5/950822.1) id HAA19114; Sat, 17 Aug 1996 07:57:58 -0400 (EDT) Received: from trypsin.chem.uit.no (trypsin.Chem.Uit.No [129.242.24.101]) by kvikk.uit.no (8.7.3/8.7.1) with SMTP id NAA20744 for ; Sat, 17 Aug 1996 13:57:57 +0200 (METDST) Received: by trypsin.chem.uit.no (911016.SGI/ABaa-2.0mini) id AA09883; Sat, 17 Aug 96 13:08:19 GMT Date: Sat, 17 Aug 96 13:08:19 GMT From: eldbjorg@chem.uit.no (Eldbjoerg S. Heimstad) Message-Id: <9608171308.AA09883@trypsin.chem.uit.no> To: chemistry@www.ccl.net Subject: protein-water interactions and force fields Non-bonded interactions between protein and water molecules: I have wondered over a long time about the accuracy of estimating the protein-water interactions of the different MM programs; parameters for VDW radius etc. I am using CHARMM or CHARMm for my studies of protein dynamics and protein stability. I assume (from the studies of Privalov & co., Khechinashvili et al.) that hydration of especially polar group may be important for the stability of the native protein structure. I have been using the SBMD method where the protein is immersed in a 34 A or 40 A radius sphere of water. Does any of you have experience or thoughts about how much the water should interact with the protein surface, how high may the RMSD level be from X-ray structure (or starting structure) during simulation (i.e. backbone atoms in a simulation of length 500 ps); is 2.5 -3.0 A a reasonable value, or ? What opininion do you have about sufficient amount of water; 10 A of water molecules beyond the protein surface, or ? I am in this case thinking about a sphere of water molecules in the connection with deformable boundaries. All opinions and experience will be highly appreciated, ####################################################### # Eldbjoerg Sofie Heimstad # # Protein Crystallography Group # # University Of Tromsoe, IMR # # 9037 Tromsoe, NORWAY phone: +47-776-45706 # # +47-776-44737 # # fax : +47-776-44765 # # E-mail: Eldbjorg.Heimstad@chem.uit.no # # URL: http://www.chem.uit.no/KJEMI/heimstad.html # ####################################################### From owner-chemistry@ccl.net Sat Aug 17 10:18:04 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id JAA19569; Sat, 17 Aug 1996 09:51:59 -0400 (EDT) Received: from schiele for MAILER-DAEMON@ccl.net by bedrock.ccl.net (8.7.5/950822.1) id JAA18730; Sat, 17 Aug 1996 09:51:59 -0400 (EDT) Received: by schiele (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) id PAA12140; Sat, 17 Aug 1996 15:48:57 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9608171548.ZM12138@schiele> Date: Sat, 17 Aug 1996 15:48:54 -0600 Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: gdch-cic@enar.organik.uni-erlangen.de, chemistry@ccl.net Subject: WWW chemical structures database extended Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit After an analysis of the logfile of the WWW chemical structures database http://schiele.organik.uni-erlangen.de/services/webmol.html we found that over 80% of the non-demo queries where name queries - which is very unfortunate, because the number of structure files on the Net which actually contain a meaningful name is rather low. Therefore, many queries to structures which are contained in the database in anonymous form did not yield results. In response to the query pattern, we have now cross-indexed the database to several catalogs of chemical manufacturers. You can now search the WWW structures database using CAS numbers and names taken from these catalogs. There are still a number of pitfalls, please read the instructions on the Web page. Please have also a look at our other WWW services (http://schiele.organik.uni-erlangen.de/services). Numerous improvements were implemented in the last weeks. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From owner-chemistry@ccl.net Sat Aug 17 15:18:11 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id OAA20262; Sat, 17 Aug 1996 14:48:38 -0400 (EDT) Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by bedrock.ccl.net (8.7.5/950822.1) id OAA19781; Sat, 17 Aug 1996 14:48:38 -0400 (EDT) Received: from judy.ic.ac.uk by punch.ic.ac.uk with SMTP (PP); Sat, 17 Aug 1996 19:48:33 +0100 Received: from cscmgb.cc.ic.ac.uk (sg1.cc.ic.ac.uk [155.198.63.8]) by judy.ic.ac.uk (8.7.5/8.7.5) with SMTP id TAA25786 for ; Sat, 17 Aug 1996 19:48:26 +0100 (BST) Received: from [155.198.63.16] by cscmgb.cc.ic.ac.uk (940816.SGI.8.6.9/4.0) id TAA11535; Sat, 17 Aug 1996 19:48:22 +0100 X-Sender: rzepa@155.198.63.8 Message-Id: In-Reply-To: <9608171548.ZM12138@schiele> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sat, 17 Aug 1996 19:45:41 +0000 To: chemistry@ccl.net From: "Rzepa, Henry" Subject: HTML, Metadata, Chemistry and Web databases Wolf-D. Ihlenfeldt writes in the message with the subject Re: CCL:WWW chemical structures database extended > the number of structure >files on the Net which actually contain a meaningful name is >rather low. Therefore, many queries to structures which >are contained in the database in anonymous form did not yield >results. One major discussion area at the moment is "metadata", defined succinctly as data about data. HTML 2 contains the option to insert into the header Most Web search engines now actively search for such metadata entries to help them produce more meaninful indices. Unfortunately, metadata is rarely used by authors. There is in fact an active group discussing how to implement this in a generic manner. This derives from some OCLC proposals called the Dublin Core metadata elements. A short summary has been prepared by myself to be discussed at the ACS nomenclature committee. Its on http://www.ch.ic.ac.uk/chemime/chemeta.html But please note its early days yet. There are some of course who are convinced that the chances of getting even 1% of authored Web documents to contain any metadata declarations is overly optimistic. I wonder whether those of you who have authored web pages and used metadata exceed that percentage? Henry Rzepa. +44 171 594 5774 (Office) +44 594 5804 (Fax) From sc18@truman.edu Sat Aug 17 23:18:11 1996 Received: from truman.edu for sc18@truman.edu by www.ccl.net (8.7.5/950822.1) id WAA21318; Sat, 17 Aug 1996 22:19:29 -0400 (EDT) Received: from modem4.truman.edu (modem4.truman.edu [150.243.101.4]) by truman.edu (8.7.5/8.7.5) with SMTP id VAA30363 for ; Sat, 17 Aug 1996 21:15:45 -0500 Message-ID: <321699E6.66D9@truman.edu> Date: Sat, 17 Aug 1996 21:19:50 -0700 From: Ken Fountain Reply-To: sc18@truman.edu Organization: Truman State University X-Mailer: Mozilla 3.0b6 (Win95; I; 16bit) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: RE: Quat N Charges Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi All, Can somebody help me with a reference to populations of quaternary ammomnium ions? I once had a reference that I stumbled all over all the time. Now I need it and can't find it. I think it was in J. Chem. Ed, but I've searched hard and not found it. Please help if you can. Sincerely, Ken Fountain sc18@truman.edu