From chemistry-request@ccl.net Fri Dec 31 16:13:41 2004 Received: from web51301.mail.yahoo.com (web51301.mail.yahoo.com [206.190.38.167]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iBVLDdkF013365 for ; Fri, 31 Dec 2004 16:13:40 -0500 Received: (qmail 97770 invoked by uid 60001); 31 Dec 2004 21:30:21 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=nyPYAdtUePdhSw+lbOUgPMLc+R0m/Ey2NgX35wcb6Ui7kjB9tDoEeZE5aj1VV2H+mt90pG97oCjKfTxdLPM1BO6J1pBcwSl57ZIFRT3uh8AUbQHBlcFycFWs/tGDQOqQwlaA+ACq+YKDWg0BXRUklSWRbCtS5aZG7PE7nP4SHs4= ; Message-ID: <20041231213021.97768.qmail/at/web51301.mail.yahoo.com> Received: from [24.152.168.117] by web51301.mail.yahoo.com via HTTP; Fri, 31 Dec 2004 13:30:21 PST Date: Fri, 31 Dec 2004 13:30:21 -0800 (PST) From: Sengen Sun Subject: CCL: Re: CCL: Unoccupied orbitals, eigenvalues To: chemistry/at/ccl.net In-Reply-To: <200412212100.iBLC4whd004878/at/maia.csd.sc.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.0 required=7.5 tests=none 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 would criticize again the claims in the Nature paper rather than blame myself for not being able to resolve the conflicts in my mind while reading the paper. Even in the abstract, the authors admited orbitals to be mathematical constructs (human-made staff). But there is not such a logic that these constructs should be observable in the nature. What they really did was to knock off a trunk of electron density by a lazer pulse. They think this trunk of electron cloud to be HOMO. They then constructed the HOMO image mathematically in such a way that the the image can fit what exists already in their minds. I would think that this is roughly a reverse process to normal computations. But the goal of normal computations is to use physically meaningless orbitals as mathematical approximation to reach some physically meaningful quantities such as electron density. The reverse process is to use the physical quantites to construct meaningless orbitals. They made the image of orbitals based on their designed math, but they did NOT image or observe them. Orbitals are not observables either in the content of QM or in the physical reality! Therefore, their claims must be criticized as they confuse chemists who have no deep knowledge of QM. The essence of what they did is drawing pictures of dreamed ghosts of no physical reality. Further, they repeated several common mistakes about the philosophical meaning of chemistry (e.g.,"To observe these orbitals change as bonds are formed and broken is to observe the essence of chemistry"). Chemistry is not about orbitals (or human made staff) but electron density and its reorganization, - the physical reality independant of human activities! Cheers for 2005! Sengen ---Original message--- From: Mikael Johansson Date: Mon, 20 Dec 2004 18:20:24 +0200 (EET) Subject: CCL: Unoccupied orbitals, eigenvalues Hello All! Catalysed by the latest in the row of experimental observations of=20 molecular orbitals (which nicely also measures the phase of the orbital)=20 [1], I again started pondering on the reality of the _unoccupied_ MO's,=20 this time especially between the qualitative difference (if any) between=20 unoccupied orbitals with negative energies versus those with positive=20 energies. Positive orbital energies for occupied orbitals indicate the=20 non-existence of the orbital, or at least the inability of the chosen=20 computational method to give a proper description of it (a larger, more=20 diffuse basis set will just throw the electron, "orbital", away from the=20 molecule) [2]. Assuming for the moment that also unoccupied (virtual) orbitals have=20 physical meaning, would then the ones with negative energies (if there=20 are any for a give species) be "more real" than the ones with positive=20 energies? I have not come across a disussion on this, or at least don't=20 remember having done so. [1] J. Itatani et al., "Tomographic imaging of molecular orbitals", Nature 432 (2004) 867-871. [2] I like the discussion in: N. R=F6sch, S.B. Trickey, J. Chem. Phys. 106 (1997) 8940-8941. Merry Christmas, Mikael J. http://www.helsinki.fi/~mpjohans/ --1824380544-1125546758-1103559624=:251477-- __________________________________ Do you Yahoo!? Yahoo! Mail - Helps protect you from nasty viruses. http://promotions.yahoo.com/new_mail From chemistry-request@ccl.net Fri Dec 31 21:55:58 2004 Received: from smg.ccnu.edu.cn ([202.114.32.6]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j012tgjb026113 for ; Fri, 31 Dec 2004 21:55:44 -0500 Received: from [202.114.32.3] by 202.114.32.6 with StormMail ESMTP id 46293.762835231; Sat, 1 Jan 2005 11:06:44 +0800 (CST) Received: from localhost (mail.ccnu.edu.cn [127.0.0.1]) by mail.ccnu.edu.cn (4U Message Server) with ESMTP id BDB36AC06E for ; Sat, 1 Jan 2005 11:07:20 +0800 (CST) Received: from qcmm9 (unknown [202.114.34.252]) by mail.ccnu.edu.cn (4U Message Server) with ESMTP id BCA43AC067; Sat, 1 Jan 2005 11:07:19 +0800 (CST) Date: Sat, 01 Jan 2005 11:13:13 +0800 To: "HU lihong" , chemistry/at/ccl.net Subject: Re: CCL:About AUTODOCK grid point References: From: scopio Organization: CCNU Content-Type: text/plain; format=flowed; delsp=yes; charset=gb18030 MIME-Version: 1.0 Message-ID: In-Reply-To: User-Agent: Opera M2/7.54 (Linux, build 751) X-Virus-Scanned: by AMaViS 0.3.12 X-Spam-Status: No, hits=6.0 required=7.5 tests=DNS_FROM_RFCI_DSN,NO_RDNS, NO_RDNS2 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 j012twjb026156 Dear Holly, Alought I'm not very familiar with your questions, I still want to share my experence with you. 1). You can modify ADT source code. Find out autogpfCommands.py located in ADT_DIR/share/lib/python2.3/site-packages/AutoDockTools. Try to locate at the following section: ----------------------------------- ifd.append({'name': 'xnumber', 'wtype':ThumbWheel, 'widgetType':ThumbWheel, #'wcfg':{'text':'number of points in x-dimension', #'wcfg':{'text':None, #'wcfg':{'text':'number of points in x', 'wcfg':{'text':None, 'showLabel':1, 'width':100, 'min':0, 'max':126, ----------------------------------- modify last line 'max':126 to any value you want. This is for X dimension, you can find similar parts for Y and Z dimension. You should use this carefully because autogrid3 might not support too large grid point unless you modify autogrid3 source code. It can be found in autodock_dir/src/autogrid/autocomm.h, keyword "MAX_GRID_PTS" 2). I still have the same question. For Phosphorus parameters, I used parameters in AMBER parm99.dat but I'm not sure if it's correct. By the way, I have tested for several times to add parameters or not add parameters, including charges and solvation paramters, the results are very similar, and looks well, for my DNA system. It's so strange.... Best Regards! Liu On Wed, 29 Dec 2004 14:42:53 +0800 (HKT), HU lihong wrote: > > Dear All, > > I have two questions about Autodock. > > (1) I am trying to docking several small ligands to a huge molecule by > AUTODOCK. But by Autodock tool, I found the maximum grid point only can > only be set to 126 in 3D. And I check the autodock manual I haven't found > there is a limit about grid point. Did anyone have similar experiences? > Could you please share them with me? > > (2)Does anyone have Phosphorus of ATP parameters? > > Thanks a lot, > > All the best, > > Holly > > > > > -= 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, jlabanow/at/nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > -- JunJun Liu College of Chemistry Central China Normal University WuHan 430079 P.R. China