From chemistry-request@server.ccl.net Sun Mar 18 04:32:04 2001 Received: from johnson.mail.mindspring.net ([207.69.200.177]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2I9W3D11285 for ; Sun, 18 Mar 2001 04:32:04 -0500 Received: from josiah (pool-63.50.172.185.dnvr.grid.net [63.50.172.185]) by johnson.mail.mindspring.net (8.9.3/8.8.5) with ESMTP id EAA06476 for ; Sun, 18 Mar 2001 04:32:00 -0500 (EST) Message-ID: <062801c0af8d$f9300fe0$b9ac323f@josiah> From: "Andrew Dalke" To: Subject: DCD and software reuse (was Qmol: Molecular viewer for Windows) Date: Sun, 18 Mar 2001 02:29:43 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Rick Venable said: >As a long time academic CHARMM user, it was *years* before it became >apparent to non-Quanta users that a DCD file was the MSI/Polygen name >for a CHARMM binary trajectory file. We always referred to them as >"trajectory files", or .trj files, an extension in common usage prior to >CHARMm, the commercial variant. I think it would be clearer if your >blurb referred to CHARMM/CHARMm explicitly, in addition to file >extension that has meaning mostly to Quanta users. I suspect part of the problem is due to "us", meaning the people at UIUC who helped write VMD, NAMD and related programs. The group was mostly XPLOR based, which shows in the use by those programs of XPLOR-specific formats. I say suspect because I see a comment in the qmol source that it bases the connectivity search from ideas in VMD so assume that part of the trajectory reading code may by similarly influenced. Quoting from the X-PLOR manual (version 3.1, chapter 11, p.143 :) The file format is identical to the CHARMm-DCD format (Brooks et. al. 1983), which can be read by QUANTA and a variety of other programs. The only exception is that the number of coordinate sets written to the trajectory is explicitly written into the header of CHARMm-DCD files, whereas XPLOR writes a zero instead. and on page 147 gives an example write trajectory output=trajectory.dcd ascii=false although on page 146 and elsewhere it uses ".crd" as an extension for a trajectory file. Since the UIUC programs all write a zero as the number of coordinate sets, that places them specifically as using the "XPLOR-DCD" format rather than "CHARMm-DCD" or "trajectory files". However, it has been a long time since I looked that that code, so I brought up the VMD ReadDCD.C code and compared it to qmol's. It appears to be a completely different implementation of reading and writing DCD files and not based on any of the UIUC code. (The coding and error checking styles are quite different from even the first version Mark Nelson wrote in 1995.) This means my assumption of an impact by the UIUC developers is wrong. Reading it over, I believe that qmol specifically parses a subset of the CHARMm trajectory format, in that it requires a count of the number of coordinate sets. In addition, I see that the VMD DCD reader has been extended to handle parts of the CHARMm trajectory format not mentioned in the XPLOR documentation, like the ability to hold an "extra block" (whatever that means) and allow 4 dimensional coordinates for the atoms. The qmol reader doesn't handle these cases. (Also, it seems there's a place where CHARMm uses a double as compared to XPLOR's float - must have been found during the conversion of the UIUC tools to 64 bit. qmol believes that number is an integer.) This whole post was really done to lead to a pet peeve of mine, which is that these formats, which we take for granted, are rarely documentated so it's often a matter of reverse engineering the binary file to figure out how things work. Even those files which are documented are not fully documented, as these special cases point out. Oh, and FORTRAN code does not make good documentation because details of FORTRAN file I/O are left up to the implementation, making it harder for C to read those files. Luckily, I believe there is an accepted standard of how to do that I/O so FORTRAN code from different vendors can talk to each other. This makes it somewhat less complicated for other languages to support those formats. Another thing which would be nice is for there to be a set of libraries for reading and writing those formats - even in FORTRAN :) That would make it easier for someone else to come along and start working with it, or at least use them as a reference. But there are obviously two major problems with that. Many groups don't release any source or when they do (and UIUC is, sadly, one of those) make it difficult to redistribute that code elsewhere. UIUC actually allows people to use and redistribute VMD code freely so long as it is a relatively minor part of both projects. The DCD reader and writer would be a small part of VMD and of qmol so would fall under that exemption. However, qmol doesn't use it and instead uses one which is more error prone, less portable, and handles only one variant of the trajectory format. Yet the API exposed by VMD's DCD reader is almost exactly superset of that needed by qmol. I don't know what can be done to limit this (in my mind) needless duplication of effort. CCL of course is one such attempt, being an archive with both messages and software. There are requests for information about various trajectory formats going back at least 6 years, but no detailed description posted (although some sources are obvious, like looking at gOpenMol because of Leif Laaksonen's requests for format descriptions; although his code doesn't explictly allow redistribution. Hmm, his code and VMD's aren't exactly the same either.) There is some source code in CCL, though most are not available as libraries. In nearly all cases, the code is quite out of date. For example, VMD is available from CCL but is at version 1.2, which is several years old. I believe this shows the CCL is not used as a primary resource for software for at least structural biology. There are other places to look for software besides CCL, but none that I know of are specific to this field. Pehaps the most relevant general site is freshmeat.net. Searching for "trajectory format" found three programs - from UIUC. For "DCD" found 3 relevant hits from 6 matches - all 3 from UIUC. For "quantum chemistry" found 1 (not from UIUC :). Searching for "Babel" found 1 relevant hit in 10 matches - to xpovchem, which uses povchem and babel. So freshmeat does not well serve this community. I must point out that the bioinformatics developers have very similar problems - undocumented formats, many diverse programs, no centralized, no recognized "portal" for information, etc. What they do have that chemistry seems to be missing are projects like bioperl, biopython, biojava, etc. which try and least to collect and develop freely available code for bioinformatics. The closest would probably be Konrad Hinsen's MMTK which focuses on strutural biology, but isn't all that useful the chemical informatics I do these days. BTW, I suspect the difference is a combination of many things. First, I believe that fewer people are developing chemistry software (MD, QC, chemical informatics, etc.) than bio (sequence analysis, gene expression, etc.) Second, I actually think chemistry software is more complicated on average!) than bioinformatics both in theory and in diversity of projects. I know that I don't want to write a QC program - MD was tricky enough. Compare also that I know 3 very distinct ways people represent molecular models (orbitals, small molecule (bond types are important) and large molecule (only atom types/force fields are important)) while there's only one general model for sequences. I suspect there are also effects because comp. chemistry is more established and has more direct ties with proprietary industry and because bioinformatics is currently getting a lot of hype and funding. There is one final option in reducing duplicitous non-science work in this field, which is to develop such a centralized site myself. I'm already working on the biopython site as well as hired by paying clients, and as Jan can no doubt point out, working on these things sucks up a lot of time. Maybe this message will prod others? Andrew Dalke dalke@acm.org P.S. BTW, on some days when I have to muck through layers of code doing who knows what, I get the feeling that we all work on top of a house of cards stuck together by voodoo. All I'm trying to to is fix the first couple of floors to make a taller building. From chemistry-request@server.ccl.net Sun Mar 18 13:22:31 2001 Received: from flu.itsc.cuhk.edu.hk ([137.189.6.46]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2IIMUD13420 for ; Sun, 18 Mar 2001 13:22:30 -0500 Received: from flu.itsc.cuhk.edu.hk (root@localhost [127.0.0.1]) by flu.itsc.cuhk.edu.hk (8.9.3/8.9.3) with ESMTP id CAA28072 for ; Mon, 19 Mar 2001 02:19:29 +0800 (HKT) Received: from l (dialup4-011.csc.cuhk.edu.hk [137.189.211.11]) by flu.itsc.cuhk.edu.hk (8.9.3/8.9.3) with SMTP id CAA28066 for ; Mon, 19 Mar 2001 02:19:27 +0800 (HKT) Message-ID: <001401c0afd8$04bd85a0$0bd3bd89@l> Reply-To: "Kiniu WONG \(Kin-Yiu\)" From: "Kiniu WONG \(Kin-Yiu\)" To: Subject: Gaussian: How can I hold initial guess symmetry? Date: Mon, 19 Mar 2001 02:19:44 +0800 Organization: Physics CUHK MIME-Version: 1.0 Content-Type: text/plain; charset="big5" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear all, From the Gaussian Manual (Gaussian 94 User's Reference P.88-89), we are able to model an excited state by transposing orbital with Guess=Alter. And it recommends use SCF=QC or SCF=DM in order to hold initial guess symmetry > from one iteration to the next. But I found that even using these two keywords, the initial symmetry is not able to be held for some molecules. So my question is: Are there any methods such that we are able to hold the initial guess symmetry with 100% certainty? I am a new to the computational chemistry. Any kinds of suggestions are useful. Thank you very much in advance. Wishes, Kiniu ---- Kiniu WONG (Kin-Yiu) Undergraduate student Department of Physics The Chinese University of Hong Kong Email: kiniu@cuhk.edu.hk or kyiwong@phy.cuhk.edu.hk From chemistry-request@server.ccl.net Sun Mar 18 16:06:15 2001 Received: from usc.edu (root@[128.125.253.136]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2IL6FD13760 for ; Sun, 18 Mar 2001 16:06:15 -0500 Received: from rcf-fs.usc.edu (root@rcf-fs.usc.edu [128.125.253.166]) by usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id NAA08620; Sun, 18 Mar 2001 13:06:15 -0800 (PST) Received: from usc.edu (IDENT:jorgevil@futura.usc.edu [128.125.14.59]) by rcf-fs.usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id NAA26557; Sun, 18 Mar 2001 13:06:15 -0800 (PST) Sender: jorgevil@rcf-fs.usc.edu Message-ID: <3AB52348.A090BE15@usc.edu> Date: Sun, 18 Mar 2001 13:06:16 -0800 From: Jordi Villa X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: mike smith CC: chemistry@ccl.net Subject: Re: CCL:experiment of H-bond strength in solution References: <20010316045354.66012.qmail@web13206.mail.yahoo.com> Hi Mike, Now that you are bringing more data to the discussion it is interesting to expand my explanations on the EVB, because I see some misunderstanding (or more likely lack of familiarity with the EVB approach) in your reply. In order to clarify your view let me point out some issues, and let others to other people more expert in the specific DNA studies. 1) Free energy calculations: H-bond in solution is a very interesting issue for computational chemistry and several methods have been employed for that. The best way to study it in solution is through reliable free energy calculations, that will account for the effect of the environment in your calculations. In this aspect, gas phase ab initio studies, although giving very important insights, are not enough to understand the physics of ion-pair separation in solution, even when microsolvation is involved in the calculations. Even current QM/MM methods are unable to solve these questions, although I am sure that in the future they will be extremely helpful. 2) Charge transfer: When studying HB, it is extremely important to take into account the charge transfer between donor and acceptor (see the original paper on the EVB (J. Am. Chem. Soc. 102, 6218 (1980)). > From this perspective, quantum calculations are desired and simple force fields would give somehow a distorted image of what is going on. Quantum calculations are, however, too expensive to perform free energy calculations. 3) merging points 1 and 2 it is clear that the EVB method is currently the method of choice, because in addition to the possible use of common force fields (see for example how Aqvist use the EVB methodology with popular force fields like AMBER) you have the ability to simulate the electronic structure of the region of interest. So, you can create your own EVB representation by simply taking your force field and trying to understand the different resonance structures involved in the chemical problem. Thus, I would think that in the lowest limit of the EVB calculations (this is, using only one resonance structure describing your system) you will reproduce the, let's say, AMBER results. The EVB can be fitted to reproduce the exact ab initio results in small clusters and also to include experimental data to produce accurate representations of the energetics of the system you are studying. An increasing number of physical chemists are moving to this representation (see for example works by Borgis, Voth, and try to see if some other force field based method can reproduce so nicely ab initio or structural data). The power of EVB is in providing in a clear way the effect of the environment on the HB's and trying to understand its physics. In deep studies one is interested in the effect of entropy, reorganization, induced dipoles...even counter-ions in the HB, and the EVB provides a natural way to incorporate these effects. 4) I hope that what I told above does not sound as cheap propaganda, this is not my purpose. In fact, the interesting two minima that you talk about are not something new. You should check, for exxample Patey & Carney, JCP, 1983, 78, 5183 or Warshel & Russell Quarterly Review of Biophysics 1984, 17, 283 (figure 18), where it is explained how an increasing improvement of the description of an ion pair in solution leads to an almost flat potential of mean force as a function of the distance. Thus, this second minima become less and less important with increasingly complex models. This is due to the compensation of the changes in the charge-charge interaction by changes in the solvation energy (see also figure 16 in the Quarterly Review). According to this, the interesting issue in the figures in J Am Chem Soc, 1999, 121, 9503 is that the first minimum is overestimated, and maybe this is an issue of bigger concern than the presence of the second minimum. 5) Thus, it is possible that the shape of the free energy calculations reported in J Am Chem Soc, 1999, 121, 9503 are due to some problems in boundary conditions or long range effects. I cannot tell you more because I saw that paper only superficially and would like to read also other explanations. 6) on the specific case of DNA I cannot tell you much and I leave the answer to other people more involved in this type of calculations, although a priori I cannot see a big difference between the general case and the DNA base pairing. I agree than in the future some study on DNA base pairing using the EVB is desirable. mike smith wrote: > Thanks a lot to Jordi & others for response! > > Since Jordi mentioned the EVB theory by Warshel, it > reminders me another method by the same group, which > is combined QM and Langevin Dipole. In J. Phys. Chem > B., 1999, 103, 884, they studied the DNA base pair > H-bond and stacking by MP2/LD. They got the potential > curves in gas phase and solution for stacking, but not > for H-bond. I guess: (1)The H-bond potential curves in > solution may be very flat, (2)the error bar of their > results could not be small, for example the free > energy for many base pairs are almost the same. (3)EVB > can't be better than MP2/LD for this problem, > otherwise, > there should already be resluts published. > > I just found another paper which is the updated > version of the Kollman's work in 1990. It's from R > Lavery's group, in J Am Chem Soc, 1999, 121, 9503. > Almost same method, same system, but with more > advanced computer power & better force field. They > gave some surprising results: in the free energy > surfaces of AT & CG in > solution, there are two minima, and two transition > states, instead of normally only one minimum for the > dissociation curve. And at the 2nd minimum, the base > pairs are separated by about 5.5 A, and it's explained > as one water forming a bridge at that distance. > > One way to confirm the 2nd minimum could be high > accuracy QM calculations, with base pair(different > distances) plus a few explicit water molecules. J. > Phys chem A, 2000, 104, 11177 can be one of the > attemps, but the bases are still very close to each > other. Hope more results could be available by that > group, or higher accuracy simulation by QM/MM with a > few explicit water > molecules in the QM region. > > --Mike > > --- Jordi Villa wrote: > > Dear Mike, > > > > One of the best ways to simulate this is by using > > the EVB method by Warshel in, > > for example: > > > > An Empirical Valence Bond Approach for Comparing > > Reactions in Solutions and in > > Enzymes, A. Warshel and R. M. Weiss, J. Am. Chem. > > Soc. 102, 6218 (1980). > > Simulation of Enzyme Reactions Using Valence Bond > > Force Fields and Other Hybrid > > Quantum/Classical Approaches, J. Åqvist and A. > > Warshel, Chem. Rev. 93, 2523 > > (1993). > > > > and specifically, on the strength of HB's, a clear > > explanation is given in: > > > > On Low-Barrier Hydrogen Bonds and Enzyme Catalysis, > > A. Warshel, A. Papazyan and > > P. A. Kollman, Science 269, 102 (1995). > > > > Also, a simplified version of the use of the EVB for > > HB's can be found at > > http://www.tanchi.com/tufts/ > > > > Hope this helps > > > > Jordi > > > > > > mike smith wrote: > > > > > Dear all, > > > > > > Since it's well-known that the H-bond strength > > will be > > > highly weaken in solution, compared with that in > > gap > > > phase, I am curious if there is any experimental > > > evidence or hint available. > > > > > > Also, I found two papers on the potential enrgy > > curves > > > of H-bond in gas-phase and solution: > > > (1)Dang, L X; Kollman, P. A, > > > J Am Chem Soc, 1990, 112,503 > > > > > > AT base pair (H-bond & stacking) > > > from 12kcal/mol(gas) to 0.8kcal/mol > > (solution) > > > > > > (2)Osapay, K; Young W S; Brooks C L; Case D A > > > J Phys Chem 1996, 100, 2698 > > > Updated in Annu Rev Phys Chem, 2000, 51, 129 > > > > > > formamide dimer > > > from 6.7 kcal/mol to 0.8 kcal/mol > > > > > > Here, I am wondering if any of you could provide > > me > > > more related reference. Also, any discussion on > > the > > > method to simulate this accurately would be highly > > > appreciated. > > > > > > Thanks for your attention! > > > > > > --Mike > > > > > > __________________________________________________ > > > Do You Yahoo!? > > > Yahoo! Auctions - Buy the things you want at great > > prices. > > > http://auctions.yahoo.com/ > > > > > > > -- > > Jordi Villa i Freixa > > jorgevil@usc.edu > > http://laetro.usc.edu/wgroup/people/jorgevil > > Department of Chemistry, University of Southern > > California > > Los Angeles, CA, USA, 90089-1062 > > Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 > > > > > > > > __________________________________________________ > Do You Yahoo!? > Get email at your own domain with Yahoo! Mail. > http://personal.mail.yahoo.com/ -- Jordi Villa i Freixa jorgevil@usc.edu http://laetro.usc.edu/wgroup/people/jorgevil Department of Chemistry, University of Southern California Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 From chemistry-request@server.ccl.net Sun Mar 18 16:48:53 2001 Received: from ns02.sbphrd.com (firewall-user@[208.198.64.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2ILmrD13835 for ; Sun, 18 Mar 2001 16:48:53 -0500 Received: by ns02.sbphrd.com; id QAA14395; Sun, 18 Mar 2001 16:48:22 -0500 (EST) From: Received: from unknown(139.136.64.5) by ns02.sbphrd.com via smap (V5.0) id xma014351; Sun, 18 Mar 01 16:48:04 -0500 Received: from uksmtp01.ha.uk.sbphrd.com (uksmtp01.ha.uk.sbphrd.com [139.136.216.185]) by phinet.sbphrd.com (8.9.1b+Sun/8.9.1) with ESMTP id QAA16919; Sun, 18 Mar 2001 16:48:14 -0500 (EST) Subject: Call for Participation: Objects in Bio- & Chem-Informatics 2001, Boston (USA), July 9-10 To: members@iscb.org, bionews@net.bio.net, corba-announce@alpha1.ebi.ac.uk, xml-dev@alpha1.ebi.ac.uk, microarray@alpha1.ebi.ac.uk, developers@alpha1.ebi.ac.uk, bioperl-announce-l@bioperl.org, biocorba-announce-l@biocorba.org, biojava-l@biojava.org, bioxml-announce-l@bioxml.org, biopython-announce-l@biopython.org, chemweb@ic.ac.uk, bioinformatics@sdsc.edu, lifesciences@omg.org, chemistry@ccl.net Cc: oibc-abstracts@omg.org Date: Sun, 18 Mar 2001 16:46:41 -0500 Message-ID: MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii We apologize to those who receive multiple copies of this email. Please distribute this call to all interested parties. ============================================ CALL FOR PARTICIPATION OBJECTS IN BIO- & CHEM-INFORMATICS 2001 (OiBC-2001) July 9 - 10, 2001 Boston, Massachusetts (USA) Organized by the Life Sciences Research Domain Task Force (LSR DTF) Sponsored by the Object Management Group (OMG) and IONA Technologies Following in the tradition of the successful 'Objects in Bioinformatics' conferences held in Hinxton, UK in 1997 and '98 and in San Jose, California in 1999, Objects in Bio- & Chem-informatics 2001 (OiBC-2001) will be held at Sheraton Ferncroft Hotel, Danvers, Massachusetts (20 minutes north of Boston) on July 9 and 10, 2001. Papers and posters reporting on original research and development of object-oriented software and systems, the role of object-oriented technology, reusable software components, design patterns, and distributed computing in life sciences research are sought. 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