From chemistry-request@server.ccl.net Fri Jan 31 00:17:32 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0V5HWj04614 for ; Fri, 31 Jan 2003 00:17:32 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h0V5HWj15964; Fri, 31 Jan 2003 00:17:32 -0500 (EST) Date: Fri, 31 Jan 2003 00:17:30 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: Sorry for CCL problems -- hard disk crushed Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL-ers Sorry to say, but we had a disk failure on CCL server... It probably happened about noon Ohio Time. Disk was rebuilt from backups, but some messages may have been lost since we do backup once a day... We are actually in the process of upgrading the whole setup, and the disk was impatient, and did not want to wait until we move stuff to another machine. Jan Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | E-mail: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/~jkl Columbus, OH 43212-1163 | http://www.ccl.net/ http://asdn.net/ From chemistry-request@server.ccl.net Fri Jan 31 04:40:23 2003 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0V9eMj22430 for ; Fri, 31 Jan 2003 04:40:22 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H9K00HQGO6KOP@mailstudenti.unimi.it> for chemistry@ccl.net; Fri, 31 Jan 2003 10:39:56 +0100 (MET) Received: from heisenberg (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H9K00B61O6LAX@smtp.unimi.it> for chemistry@ccl.net; Fri, 31 Jan 2003 10:39:57 +0100 (MET) Date: Fri, 31 Jan 2003 10:43:54 +0100 From: Alessandro Contini Subject: Re: CCL:Phosphoserine parameters In-reply-to: To: Karthikeyan Swaminathan Cc: CCL Message-id: <200301311043.54194.alessandro.contini@unimi.it> Organization: Istituto di Chimica Organica "Alessandro Marchesini" MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 User-Agent: KMail/1.4.3 References: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h0V9eNj22431 Dear Karthikeyan , I'm having done the same for phosphotyrosine. I didn't found parameters so I derived them. This is the procedure I used, but is the first time that I do parametrization so take it with care: First I built the fosforilated residue using leap and I pretected it with ACE and NME protecting groups. I build 3 versions of the Posphate moiety: as free anion, as H2Phosphate and as Na2Phosphate. I used GAMESS to optimize geometry at HF/6-31G* level. The free anion, as expected, resulted in a distorted geometry due to the interaction of the PO3 with amidic NH. Then I removed phosphate H or Na and I used antechamber to make an input for a SP calculation with G98. The trick could be removing protections before building the prep file; i genereted a preliminary .prep for PTR with leap, than I used antechamber for generating the .prep from G98 and then I matched the two preps. Use parmchk and parmcalc for deriving missing parameters (take those from the ab-initio calculation), then you are done. Hope this help Alessandro For me this worked Alle 00:37, venerdì 31 gennaio 2003, Karthikeyan Swaminathan ha scritto: > Dear all, > > Can someone send me or tell me where I can find force field parameters for > Phosphoserine in Amber force field format. > I am trying to run some dynamics after phosphorylation. > > Thanks in advance. > Karthik. > > > Swaminathan, Karthikeyan > Graduate Student > Univ. of Cincinnati > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net -- Dott. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm