From chemistry-request@server.ccl.net Sun Oct 28 00:15:05 2001 Received: from janus.hosting4u.net ([209.15.2.37]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9S4F4B08633 for ; Sun, 28 Oct 2001 00:15:05 -0400 Received: (qmail 7797 invoked from network); 28 Oct 2001 04:18:03 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 28 Oct 2001 04:18:03 -0000 Received: from yersina ([210.50.57.44]) by proinformatix.com ; Sat, 27 Oct 2001 23:17:47 -0500 Reply-To: From: "Sergio Manzetti" To: "Chemistry Discussion G" Cc: "Gromacs Mailring" Subject: Heme groups in GROMACS Date: Sun, 28 Oct 2001 13:14:37 -0800 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Hi every1. Has anyone perfromed molecular simulations with HEME groups, and experienced problems with it? Whatever I do, minimize 1 time, or 3000 steps I get deviation of bond lengths of unacceptable nature, at the beginning of the simulation. Sergio ____________________________________________________________________________ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Sun Oct 28 16:57:31 2001 Received: from VAX.PHR.UTEXAS.EDU ([128.83.164.1]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9SLvUB28688 for ; Sun, 28 Oct 2001 16:57:30 -0500 Received: by VAX.PHR.UTEXAS.EDU for chemistry@ccl.net; Sun, 28 Oct 2001 17:05:34 -0600 Date: Sun, 28 Oct 2001 17:05:34 -0600 From: PEARLMAN@VAX.PHR.UTEXAS.EDU To: chemistry@ccl.net CC: PEARLMAN@VAX.PHR.UTEXAS.EDU Message-Id: <011028170534.10540@VAX.PHR.UTEXAS.EDU> Subject: Re: CCL:Ring perception algorithm Hello -- I am woefully behind with respect to e-mail and, consequently, I just saw the message which Mark Thompson posted on at Fri, 19 Oct 2001 11:43:29 -0700: > I would like to hear from anyone who has implemented the ring perception > algorithm of Balducci and Pearlman (1994). I have some interesting > questions and observations to share. 11 minutes and 27 seconds earlier (i.e., at Fri, 19 Oct 2001 11:32:02 -0700), Mark sent the following message directly to me. It includes the questions to which he alluded in his CCL posting. I suspect that the answer to his questions might be of interest to anyone else interested in ring perception and, hence, I'm responding to Mark's questions now: > Dear Prof. Pearlman, > > I have had great fun implementing and using the algorithm from Balducci > & Pearlman J. Chem. Imf. Comput. Sci. 1994, 34, 822-831. > > I was hoping I could bother you with two questions. > > 1. I am interested in finding out contact information for Dr. Balducci, > if it is available. > > 2. I have had some difficulty with certain classes of molecules and the > algorithm in the above paper: specifically, fullerenes like buckyball. > Generally, all, but 1 of the rings are found. So for buckyball the > formula in your paper gives 31 rings (R = E - N + 1 = 31) when there > are 32 rings in this structure (at least to a chemist, but perhaps not > to a mathematical topologist). The math in the algorithm appears to be > straightforward and I've rechecked everything many times by hand. Has > this issue ever cropped up in your use of the method? I think zeolites > and other clathrate type molecules would present problems as well. > > Sincerely, > Mark Thompson Answers: 1. Renzo Balducci was my grad student when we developed the algorithm to which Mark refers. He remained in my Lab as a postdoc while waiting for his wife to complete her Ph.D.. When his wife then chose to take a postdoctoral position near Austin, Renzo decided to remain in my Lab as a permanent Research Associate and he remains a highly valued member of our group. You can reach him at balducci@naphthyl.phr.utexas.edu. 2. Although we developed a novel derivation of the "R = E - N + 1" equation which is the central point of Mark's question, that equation is the well-known Euler's Theorem first derived by Leonhard Euler over 250 years ago. Our algorithm identifies the smallest set of smallest rings (SSSR) of a molecular connection table (or any other topological graph of nodes and edges). This is a classic problem in graph-theory and, prior to the publication of our algorithm and associated proof, it was thought to be a member of a class of "NP-complete" problems. Previously, SSSR perception programs either implemented exact solutions which required cpu-times which increased exponentially with the size of the ringsystem or they implemented faster but non-exact solutions which could easily miss finding the true SSSR. Our solution was based on a novel "chain-message" algorithm which we proved provides an exact solution of polynomial (roughly N*logN) order. Significantly, our contribution was to discover a new algorithm to identify *which* rings comprise the SSSR but the *number* of rings in the SSSR is determined by Euler's Theorem. The SSSR is comprised of the set of smallest linearly independent -- i.e., *non-redundant* -- rings. Mark Thompson deserves credit for wondering if the answer to his question (about 31 vs 32 rings in "buckyball") might be found in the difference between a typical chemist's perception of "caged" ringsystems and the undeniably correct topological representation of such structures. Although *exactly* the same explanation would apply in the case of any other "caged" structure (such as Mark's buckyball), the explanation is easiest to make and understand if we simply talk about cubane. The eight carbon atoms of cubane form a cube with six faces. Hence, most chemists would, at first, say that cubane consists of six 4-membered rings. But it is easy to see that, once five sides of the "box" have been defined, the sixth side is also defined! (That is, all four atoms and all four bonds between the atoms of the sixth side have already been defined and used when constructing other sides of the cube.) Note that Euler's Theorem yields R = 12 - 8 + 1 = 5 rings for cubane (just as our algorithm would find and report). Lastly, I can not resist pointing out that structures which chemists justifyably regard as "cages" (such as cubane or buckyball) can and, in some respects, should be regarded as planar fused ringsystems. Imagine drawing the "front" face of a cube as a large dark square, drawing the "back" face as a smaller lightly-drawn square centered inside the first square, and drawing the other faces by making tapered connections from the corners of the outer square to the corners of the inner square. Now, replace all of the dark, light, and tapered "bonds" (edges) with lines of uniform width and intensity and note that the resulting planar fused ringsystem is topologically equivalent to the cube. Hence, neither our ring perception algorithm nor Euler's Theorem see fullerenes or any other "caged" ringsystems as particularly "tricky" problems because, in fact, they are no different than non-tricky ringsystems. I hope that my comments have been of interest to some of you. Also, if anyone else has questions or has encountered any difficulty when implementing our "chain message" algorithm, please don't hesitate to contact me. Best wishes, -- Bob Pearlman Robert S. Pearlman, Ph.D Coulter R. Sublett Regents Chair in Pharmacy and Director, Laboratory for the Development of Computer-Assisted Drug Discovery Software College of Pharmacy University of Texas Austin, Texas 78712 512-471-3383 (voice) 512-471-7474 (FAX) pearlman@naphthyl.phr.utexas.edu From chemistry-request@server.ccl.net Sun Oct 28 20:09:30 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9T19UB02787 for ; Sun, 28 Oct 2001 20:09:30 -0500 Received: from eyou.com ([61.136.62.74]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with SMTP id UAA27417 for ; Sun, 28 Oct 2001 20:09:28 -0500 (EST) Received: (qmail 25459 invoked by alias); 29 Oct 2001 09:12:25 +0800 Received: from unknown (HELO eyou.com) (172.16.2.1) by 172.16.1.2 with SMTP; 29 Oct 2001 09:12:25 +0800 Received: (qmail 501 invoked by uid 65534); 29 Oct 2001 09:12:25 +0800 Date: 29 Oct 2001 09:12:25 +0800 Message-ID: <20011029091225.500.qmail@eyou.com> From: "王明韬" To: CHEMISTRY@ccl.net Reply-To: "王明韬" Subject: for help Dear all: How can I develop the forcefield parameters of Co(II)? Thanks! Wang --http://www.eyou.com --稳定可靠的免费电子信箱 语音邮件 移动书签 日历服务 网络存储...亿邮未尽 From chemistry-request@server.ccl.net Sun Oct 28 17:43:58 2001 Received: from hotmail.com ([64.4.9.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9SMhwB29769 for ; Sun, 28 Oct 2001 17:43:58 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sun, 28 Oct 2001 14:46:52 -0800 Received: from 129.82.79.72 by lw9fd.law9.hotmail.msn.com with HTTP; Sun, 28 Oct 2001 22:46:52 GMT X-Originating-IP: [129.82.79.72] From: "Elena Jakubikova" To: elfy04@matematicas.udea.edu.co, chemistry@ccl.net Subject: Re: CCL:Gaussin intallation Date: Sun, 28 Oct 2001 15:46:52 -0700 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 28 Oct 2001 22:46:52.0808 (UTC) FILETIME=[6FFC2080:01C16002] Hi I don't think your problem is in the library version. To install Gaussian on Red Hat 7.0 you don't need only blas-f2c.a library, but also Portland Group Fortran compiler 3.2-4 (the makefile doesn't run with the standard linux fortran compiler). But even though you get the PGI compiler (by the way you need to buy it - if you get just trial version and compile the program with it, after 15 days it will not run anymore), there is a file dclock.s you need and which is not included in the new version of PGI. However, your trouble doesn't end here - the makefile included with program does not work for Red Hat 7.0. In order to make it run you will need to make some changes in mdutil.c and and get new i386.make from Gaussian (they have been really helpful with this part). However, if you choose to go to the older version of Red Hat - like 6.2, it will save you the trouble with changing the makefile. Also there is a possibility you write your own makefile and compile it with the linux fortran compiler, but in this case your program will run slower. By the way I did the instalation this way on pentium III processor, but I imagine it doesn't make much difference - the problem is not the processor, but the oprating system. Hope you find this helpful Elena Jakubikova _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp