From chemistry-request@ccl.net Mon Jan 17 21:52:03 2005 Received: from bwebmail2.gabia.com ([211.43.212.209]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0I2pxxf019513 for ; Mon, 17 Jan 2005 21:52:00 -0500 Received: (hhosting 11856 invoked from network); 18 Jan 2005 11:51:53 +0900(KST) Received: from unknown (HELO arcadia) (tblee-.at.-insilicotech.co.kr@218.148.24.166) by 211.43.212.209 with SMTP; Tue, 18 Jan 2005 02:51:53 +0000 From: "Tae-Bum Lee" To: Subject: angle measurement Date: Tue, 18 Jan 2005 11:51:53 +0900 Message-ID: <000001c4fd08$aad15df0$a064a8c0@arcadia> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Spam-Status: No, hits=6.1 required=7.5 tests=DATE_IN_PAST_06_12,NO_RDNS2, RCVD_IN_DSBL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLer ! How I can do all angle measurement in 3-D model from the pdb format or cartesian coordinate ? Isn't there any code to make full list of angle generation ? Regards, Tae-Bum From chemistry-request@ccl.net Tue Jan 18 06:33:59 2005 Received: from deluge.umist.ac.uk (deluge.umist.ac.uk [130.88.120.66]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0IBXwKN013999 for ; Tue, 18 Jan 2005 06:33:58 -0500 Received: from webmail1.manchester.ac.uk ([130.88.204.17]) by deluge.umist.ac.uk with esmtp (Exim 4.43) id 1CqrcR-0006yS-AV for chemistry-.at.-ccl.net; Tue, 18 Jan 2005 11:33:55 +0000 Received: by webmail1.manchester.ac.uk (Postfix, from userid 30) id 8BC5A8000ED; Tue, 18 Jan 2005 11:33:57 +0000 (GMT) Received: from host81-134-229-140.in-addr.btopenworld.com (host81-134-229-140.in-addr.btopenworld.com [81.134.229.140]) by webmail1.manchester.ac.uk (Horde) with HTTP ;Tue, 18 Jan 2005 11:33:57 +0000 Message-ID: <20050118113357.db5s0g4cgs0484gk-.at.-webmail1.manchester.ac.uk> X-Priority: 3 (Normal) Date: Tue, 18 Jan 2005 11:33:57 +0000 From: Richard Greaves To: chemistry-.at.-ccl.net Subject: Targeted Molecular Dynamics with CHARMM MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-15 Content-Disposition: inline Content-Transfer-Encoding: 7bit User-Agent: Internet Messaging Program (IMP) 4.0-cvs X-Originating-IP: 81.134.229.140 X-Spam-Status: No, hits=6.6 required=7.5 tests=NO_RDNS2,PRIORITY_NO_NAME, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I am looking into the possibility of running targeted (or steered) MD simulations to model the transitions between states in a multi-state structural cycle. I know that Schlitter et al J Mol Grap 12 84-89 1994, implemented TMD in GROMOS but I only have access to a rather old version of CHARMM (22 I believe, but would need to check). I have come across a constraint command in CHARMM RGYR FORCE x REFE y RMSD ... etc which looks like it might be suitable for this purpose. I'm guessing that the RMSD constraint is used to minimize the RMSD between the current structure and the reference (in this case the target or final state). can anyone tell me if it will be reasonable to run TMD using this command in CHARMM? Regards, Dr Richard Greaves. R.Greaves-.at.-manchester.ac.uk From chemistry-request@ccl.net Tue Jan 18 09:33:24 2005 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0IEXNKN023395 for ; Tue, 18 Jan 2005 09:33:23 -0500 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 1CquPZ-0007nd-6B for chemistry-.at.-ccl.net; Tue, 18 Jan 2005 10:32:49 -0400 Received: from 129.173.17.153 ( [129.173.17.153]) as user smlpnt-.at.-mailserv.mta.ca by webmail.mta.ca with HTTP; Tue, 18 Jan 2005 10:32:49 -0400 Message-ID: <1106058769.41ed1e1125b18-.at.-webmail.mta.ca> Date: Tue, 18 Jan 2005 10:32:49 -0400 From: smlpnt-.at.-mta.ca To: chemistry-.at.-ccl.net Subject: ONIOM with fixed parameters MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 129.173.17.153 X-Spam-Status: No, hits=2.0 required=7.5 tests=IMPRONONCABLE_1,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Is it possible to fix bond lengths and angles in the high level of an ONIOM calculation? From chemistry-request@ccl.net Tue Jan 18 05:15:22 2005 Received: from web1.ulb.ac.be (iee.ulb.ac.be [164.15.59.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0IAFLKN010569 for ; Tue, 18 Jan 2005 05:15:22 -0500 Received: from wwwdev.ulb.ac.be (resu1 [164.15.59.200]) by web1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id LAA25140; Tue, 18 Jan 2005 11:15:20 +0100 (MET) for chemistry.-at-.ccl.net Date: Tue, 18 Jan 2005 11:15:20 +0100 (MET) Message-Id: <200501181015.LAA25140.-at-.web1.ulb.ac.be> From: Christophe Biot To: chemistry.-at-.ccl.net X-sender-IP: 194.167.99.112 Subject: porphyrin X-Mailer: Webmail ULB v2.1 X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All, I would like to perform an analysis of the geometrical and electronic structure of some iron-porphyrin derivatives. Could someone advise me about the method of choice (DFT, HF, MP2...) for such kind of calculation? And also about the basis set (Lanl2dz, LanL2dm, SDD, ...) to use? regards christophe From chemistry-request@ccl.net Mon Jan 17 22:11:52 2005 Received: from kc-msxproto3.kc.umkc.edu (kc-msxproto3.kc.umkc.edu [134.193.44.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0I3BpKN020504 for ; Mon, 17 Jan 2005 22:11:51 -0500 Received: from KC-MAIL5.kc.umkc.edu ([134.193.32.2]) by kc-msxproto3.kc.umkc.edu with Microsoft SMTPSVC(6.0.3790.0); Mon, 17 Jan 2005 21:11:50 -0600 X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: orbitals and reality Date: Mon, 17 Jan 2005 21:11:50 -0600 Message-ID: <7E64C424A9A62B4592CC505FD28982074A4348.-at-.KC-MAIL6.kc.umkc.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: orbitals and reality Thread-Index: AcT88UkeHONmgAEtRAeETZQbeScCkAAGTwWk From: "Yang, Shizhong" To: "Sengen Sun" , X-OriginalArrivalTime: 18 Jan 2005 03:11:50.0895 (UTC) FILETIME=[742F6FF0:01C4FD0B] X-Spam-Status: No, hits=4.5 required=7.5 tests=FROM_HAS_MIXED_NUMS,NO_RDNS2, SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j0I3BqKN020508 Sengen: I disagree with your opinions. Two reasons are: 1. Although there is some confusion in that nature paper's explaination of what they are doing, what they are trying to express is just what they had done experimentally. 2. 'To see' molecule orbitals, in some sense not fully the same, is very similar to 'seeing electric field or magnetic field' in our under experimental labs. I thought their ideas should be highly respectible. SY ________________________________ From: Computational Chemistry List on behalf of Sengen Sun Sent: Mon 1/17/2005 4:46 PM To: chemistry.-at-.ccl.net Subject: CCL:orbitals and reality I have been asked to make a summary on this year discussion on this subject. I received responces from 10 this year. 3 of them are neutral, 5 agree, and 2 disagree. I am specially interested in the disagreements and therefore post them here. I would think the first one might be meaningful. And we will have to see. I would be much happier if Mikael P Johansson and any one else could also critisize my earlier postings on the List as well :-). Here are two examples: http://www.ccl.net/cgi-bin/ccl/message.cgi?2003+07+28+001; http://www.ccl.net/cgi-bin/ccl/message.cgi?2003+06+02+016; The second disagreement is not specific enough. But I will address it later after Mikael P Johansson's next message or posting. Cheers! Sengen --- Mikael P Johansson wrote: > Well, if it helps, I disagree with you :-) I will > write up a "pro-orbital" > mail for CCL as soon as my work load permits. > > Happy New Year, > Mikael J. > http://www.helsinki.fi/~mpjohans/ > --- @yahoo.com> wrote: > Hello Dr. Sun, > > It's interesting to see your posts about that paper. > > > Since I am very busy I have not read the details of > the paper. However it > looks like what they did in the paper is very > important and meaningful. > > I think they derived some information about the > orbital from experiments > and data analysis, similar to the X-ray data > analysis in some sense. Also > they mentioned that the phase component of the wave > function is arbitary. > Very likely they derived the real part or the > imaginative part, or at > least some of either. So it's still very meaningful > > __________________________________ Do you Yahoo!? Yahoo! Mail - 250MB free storage. Do more. 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