From chemistry-request@ccl.net Mon Oct 6 22:05:29 2003 Received: from ns1.scripps.edu (ns1.scripps.edu [192.42.82.59]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9724w59009269 for ; Mon, 6 Oct 2003 22:04:58 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.7/TSRI-4.2rx) with SMTP id h9724wL23974 for ; Mon, 6 Oct 2003 19:04:58 -0700 (PDT) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 22596; Mon, 06 Oct 2003 19:07:10 -0700 (PDT) Received: from klee.scripps.edu (klee [137.131.252.148]) by relay2.scripps.edu (8.11.7/TSRI-4.4.1rAVB) with ESMTP id h9724sR19673 for ; Mon, 6 Oct 2003 19:04:54 -0700 (PDT) Received: from scripps.edu (klee.scripps.edu [137.131.252.148]) by klee.scripps.edu (Postfix) with ESMTP id 3D9FB4A206 for ; Mon, 6 Oct 2003 19:04:54 -0700 (PDT) Message-ID: <3F821F45.5000300$at$scripps.edu> Date: Mon, 06 Oct 2003 19:04:53 -0700 From: Craig Shepherd User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry$at$ccl.net Subject: Atomic contact energies Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello all, Does anyone know of a program (standalone or incorporated into some package) that will calculate atomic contact energies (ACE) for a protein structure(s)? It seems that a lot of docking groups use them in their scoring functions, so my hunch is the programs are out there. So you know what I'm talking about, the ACE's I'm talking about are described in the following references: Miyazawa, S. and Jernigan, R.L. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. 1985. /Macromolecules/ 18:534-552. Zhang, C. /et al. /Determinations of atomic desolvation energies from the structures of crystallized proteins. 1997. /J. Mol. Biol. /267:707-726. Thanks a lot, Craig Shepherd From chemistry-request@ccl.net Tue Oct 7 00:03:25 2003 Received: from yangtze.hku.hk (yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9742q59011971 for ; Tue, 7 Oct 2003 00:02:53 -0400 Received: from localhost (lhhu@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id h974M9e01732 for ; Tue, 7 Oct 2003 12:22:09 +0800 Date: Tue, 7 Oct 2003 12:22:09 +0800 (HKT) From: Hu LiHong To: chemistry$at$ccl.net Subject: BR parameter in CHARMM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear All, Can someone give me the BR parameter (include charge parameters)in Charmm calculation? Thanks a lot Have a nice day, Carol From chemistry-request@ccl.net Tue Oct 7 04:30:50 2003 Received: from mail.fescomail.net ([202.94.7.253]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h978UD59017874 for ; Tue, 7 Oct 2003 04:30:18 -0400 Message-Id: <200310070830.h978UD59017874^at^server.ccl.net> Received: (qmail 96779 invoked by uid 2000); 7 Oct 2003 16:31:02 -0000 Received: from unknown (HELO xx-lbpctw157to8) (202.103.38.170) by 192.168.4.11 with SMTP; 7 Oct 2003 16:31:02 -0000 From: "xiongying" To: "CHEMISTRY^at^ccl.net" Subject: CCL: how to do calculations of enzyme with ONIOM method X-mailer: Foxmail 4.2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Date: Tue, 7 Oct 2003 16:32:26 +0800 X-Spam-Status: No, hits=2.9 required=7.0 tests=DATE_IN_PAST_06_12,FROM_ENDS_IN_NUMS,RCVD_IN_RFCI version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) CHEMISTRYHi, everyone, I just want to do the geometry optimization with ONIOM method using Gaussian.However, I met some problems: (1) How to decide the charge of enzyme ? How to decide the charge of every layer? (2)When I begin to run Gaussian, I consider all the system as one layer for a try with Dreiding force field.However I got the following error information: Unrecognized type string: ZR3_4 Unrecognzied type string in DecAty. Thank you for your time! From chemistry-request@ccl.net Tue Oct 7 10:31:39 2003 Received: from smtp.goldrush.com (smtp.goldrush.com [206.171.171.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h97EV759027263 for ; Tue, 7 Oct 2003 10:31:08 -0400 Received: from goldrush.com (x2-04-132.goldrush.com [64.162.10.132]) by smtp.goldrush.com (8.11.6/8.11.6) with ESMTP id h97EV5C00752; Tue, 7 Oct 2003 07:31:05 -0700 Date: Tue, 7 Oct 2003 07:30:25 -0700 Subject: Re: CCL:AM1, MNDO and PM3 software Content-Type: text/plain; delsp=yes; charset=ISO-8859-1; format=flowed Mime-Version: 1.0 (Apple Message framework v551) Cc: chemistry:at:ccl.net To: =?ISO-8859-1?Q?"Gon=E7alo_Deira_Justino"?= From: Stephen Bowlus In-Reply-To: Message-Id: X-Mailer: Apple Mail (2.551) X-MailScanner: Found to be clean X-MailScanner-SpamCheck: not spam (whitelisted), SpamAssassin (score=0, required 4.2) X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES,USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h97EVd59027280 Depending on your OS, there are several incarnations of MOPAC available. Most are built on MOPAC 6, which is a wonderfully stable code. Personally, I use an older version of MacSpartan from Wavefunction (this is on a Mac G3 with Mac OS 9), with some work being done in WinMopac. For Windows, look at WinMopac, which is available free on the Web. For Linux/UNIX, there are too many to count, altogether too many of which have been tinkered with. If you have compilers and all, I would recommend getting a virgin copy from CCL or QCPE, and building your own executable ... you get the manual that way, too! If you are not a developer, resist the temptation to use MOPAC 7, which was not intended as a production version. Getting entropy and stuff in MOPAC involves doing a very rigorous geometry optimization, then a force and thermodynamics calculation. This can all be done in the same run, with the correct selection of keywords, and paging through the voluminous output. Hope this helps, Steve On Monday, October 6, 2003, at 09:46 AM, Gongalo Deira Justino wrote: > Dear CCL, > > I'm currently using AM1, MNDO and PM3 methods to optimize > molecular geometries. Can you tell me any software, > preferentially free, but not only, that does this? If it also > allows me to get entropy and related stuff, it'd be cool. > > Thanks > Gongalo > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY:at:ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST:at:ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl:at:ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > >