From chemistry-request@server.ccl.net Tue Jun 26 03:35:28 2001 Received: from md.huji.ac.il ([132.64.169.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5Q7ZR502201 for ; Tue, 26 Jun 2001 03:35:28 -0400 Received: from localhost (anvarr@localhost) by md.huji.ac.il (8.9.3/8.9.3) with ESMTP id KAA657141; Tue, 26 Jun 2001 10:35:18 +0300 (IDT) Date: Tue, 26 Jun 2001 10:35:18 +0300 From: Anwar Rayan To: bxiong cc: "chemistry@ccl.net" Subject: Re: CCL:X-mailer: FoxMail 3.0 beta 2 [cn] In-Reply-To: <200106250911.RAA04598@mail.shcnc.ac.cn> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 25 Jun 2001, bxiong wrote: > Dear Members: > because my residue in the protein is a non-normal amino acid , >so the AMBER can not recognize it .I want to fit the charge . but I can >not determine what structure I use? Is I use the whole residue which have >the normal COOH and NH2 or I use the structure which deleted OH and >H(NH2) ? Can anyone give me suggestion about how to calculate charge of >it ? You should use the non-normal amino acid blocked by two blocking groups: 1- C(O)CH3 connected to the N-terminal 2- NHCH3 connected to the C-terminal Cheers, Anwar Rayan ------------------------------------- Dr. Anwar Rayan Department of Medicinal Chemistry School of Pharmacy The Hebrew University of Jerusalem P.O.B. 12065 Jerusalem 91120 Israel Tel: +972-2-6757539 Mobile: +972-55-848338 Email: anvarr@md.huji.ac.il ------------------------------------- > > > > > Best regards! > > bxiong@mail.shcnc.ac.cn > > Xiong Bin > Shanghai Institute of Materia Medica, C.A.S. > phone:021-64311833-222(office) > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody| CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net| WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Tue Jun 26 11:57:04 2001 Received: from web12705.mail.yahoo.com ([216.136.173.242]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5QFv3522362 for ; Tue, 26 Jun 2001 11:57:03 -0400 Message-ID: <20010626155702.32125.qmail@web12705.mail.yahoo.com> Received: from [129.105.55.29] by web12705.mail.yahoo.com; Tue, 26 Jun 2001 08:57:02 PDT Date: Tue, 26 Jun 2001 08:57:02 -0700 (PDT) From: water Miller Subject: How to implement quenching in a MD? To: CHEMISTRY@ccl.net In-Reply-To: <3B3790F2.9C2EDDA4@mail.chem.tamu.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear folks, Could any of you please teach me how to use quenching? I was told it's a good choice for locating local minimum, but don't know the detail of the algorithm. Thank you so much in advance! Water Miller __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Tue Jun 26 03:25:52 2001 Received: from lancelot.imb-jena.de ([192.124.248.76]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5Q7Pp502081 for ; Tue, 26 Jun 2001 03:25:52 -0400 Received: (from pineda@localhost) by lancelot.imb-jena.de (SGI-8.9.3/8.8.8) id JAA56715; Tue, 26 Jun 2001 09:25:28 +0200 (CEST) From: pineda@imb-jena.de (Felipe Pineda) Message-Id: <10106260925.ZM156637@lancelot.imb-jena.de> Date: Tue, 26 Jun 2001 09:25:28 +0000 In-Reply-To: bxiong "CCL:X-mailer: FoxMail 3.0 beta 2 [cn]" (Jun 25, 5:06pm) References: <200106250911.RAA04598@mail.shcnc.ac.cn> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: bxiong , "chemistry@ccl.net " Subject: Re: amber charges Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii hi Bin! take a look at http://amber.ch.ic.ac.uk/charges.txt hope it helps best regards felipe On Jun 25, 5:06pm, bxiong wrote: > Subject: CCL:X-mailer: FoxMail 3.0 beta 2 [cn] > Dear Members: > because my residue in the protein is a non-normal amino acid ,so the AMBER can not recognize it .I want to fit the charge . but I can not determine what structure I use? Is I use the whole residue which have the normal COOH and NH2 or I use the structure which deleted OH and H(NH2) ? Can anyone give me suggestion about how to calculate charge of it ? > thanks!!! > > > > > Best regards! > > bxiong@mail.shcnc.ac.cn > > Xiong Bin > Shanghai Institute of Materia Medica, C.A.S. > phone:021-64311833-222(office) > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >-- End of excerpt from bxiong -- ********************************************************************** * Felipe Pineda,PhD * * Institut fuer Molekulare Biotechnologie * * AG Theoretische Biophysik * * Beutenbergstrasse 11, Jena Vox: +49-3641-65-6491 * * Postfach 100 813, D-07708 Jena, Germany Fax: -6495 * * web: www.imb-jena.de/~pineda * * "The problem with being on the cutting edge is that you * * occasionally get sliced from time to time..." * ********************************************************************** ********************************************************************** * DISCLAIMER: Unless indicated otherwise, everything in this note is * * my personal opinion, not an official statement of my employer * **********************************************************************