From chemistry-request@server.ccl.net Sun May 2 11:09:55 1999 Received: from jg1.bchem.temple.edu (jg1.bchem.temple.edu [155.247.44.101]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA25551 for ; Sun, 2 May 1999 11:09:54 -0400 Received: by jg1.bchem.temple.edu (931110.SGI/911001.SGI) for CHEMISTRY@ccl.net id AA18390; Sun, 2 May 99 02:09:45 -0700 Date: Sun, 2 May 99 02:09:45 -0700 From: gabriel@jg1.bchem.temple.edu (Dr. Jerome L. Gabriel) Message-Id: <9905020909.AA18390@jg1.bchem.temple.edu> To: CHEMISTRY@ccl.net Subject: prediction of metabolic breakdown of drugs I would like to say thank you to all who responded to my inquiry. "I would appreciate some help in finding references and/or computer programs that would help in the prediction of the metabolic breakdown of drugs and other pharmacological compounds." RESPONSES (1) Check out METABOLITE by MDL. (2)Prof. Klopman's group at Case Western Reserve University has been developinga software called META to predict xenobiotics metabolism. You may check the following references: 1. Klopman, G., M. Dimayuga, et al. (1994). "META. 1. A Program for the Evaluation of Metabolic Transformation of Chemicals." J. Chem. Inf. Comput. Sci. 34: 1320-1325. 2. Talafous, J., L. Sayre, et al. (1994). "META. 2. A Dictionary Model of Mammalian Xenobiotic Metabolism." J. Chem. Inf. Comput. Sci. 34: 1326-1333. 3. Klopman, G., M. Tu, et al. (1997). "META 3. A Genetic Algorithm for Metabolic Transform Priorities Optimization." J. Chem. Inf. Comput. Sci 37(2): 329-334. Check his homepage for more information of this program at http://www.multicase.com. Meihua Tu Ph.D. In Computational Chemistry ROW Sciences, INC NCTR/FDA (3)Probably the best program available is META, from MultiCASE, Inc. (http://www.multicase.com). The code is explained in a series of papers: Klopman, Dimayuga & Talafous, J. Chem. Inf. Comput. Sci. 34:1320-25 (1994) Talafous, Sayre, Mieyal & Klopman, J. Chem. Inf. Comput. Sci. 34:1326-1333 (1994) Klopman, Tu and Talafous, J. Chem. Inf. Comput. Sci. 37:329-34 (1997) John Manchester Staff Scientist, Camitro Corp. t;877-CAMITRO; f:781-453-1988 john.manchester@camitro.com From chemistry-request@server.ccl.net Wed Apr 28 17:00:35 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA12892 for ; Wed, 28 Apr 1999 17:00:34 -0400 Received: from giasbma.vsnl.net.in (giasbma.vsnl.net.in [202.54.4.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA07674 Wed, 28 Apr 1999 16:57:19 -0400 (EDT) Received: from giasbmc.vsnl.net.in (giasbmc [202.54.4.6]) by giasbma.vsnl.net.in (8.8.8/8.8.8) with SMTP id CAA21744 for ; Thu, 29 Apr 1999 02:36:09 +0500 (IST) Date: Thu, 29 Apr 1999 02:07:34 -0500 (GMT) From: Amit Galande To: chemistry@www.ccl.net Subject: rational sampling Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am looking for some refernces where by I will come to know the following information regarding various softwares used for sampling combinatorial libraries 1)their names 2)time they require for sampling say around 10k molecules(or any specified no. you know) 3)percentage overlap they permit when they do sampling rationally (it can never be 0%, I suppose)(It may vary from library to library but I am looking for general range that these softwares give) 4)For a given specified library,the number of molecules they pick up(from 10k or any specified no.) to make the subset most diverse and minimum in number and if possible description of such libraries. (I agree that the no. of molecules a subset will have from 10k molecules will differ depending clustering in the library but if you have some references regarding work done by someone on specific libraries to calculate subset and other above mentioned factors then such refernces are most welcome. Thanking you in anticipation Amit k. Galande From chemistry-request@server.ccl.net Wed Apr 28 21:44:06 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA15015 for ; Wed, 28 Apr 1999 21:44:06 -0400 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA14588 Wed, 28 Apr 1999 21:40:31 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA15308; Thu, 29 Apr 99 09:39:27 -0700 Date: Thu, 29 Apr 1999 09:39:27 -0700 (PDT) From: Arthur Wang To: CCL Subject: Release of LigBuilder beta version Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, We would like to announce that the beta version of LigBuilder is now available to the public. LigBuilder is a general-purposed program package written for structure -based drug design procedure. Based on the 3D structure of the target protein, it can automatically build ligand molecules within the binding pocket. Manuscripts describing LigBuilder in details are currently under preparation. In brief, main features of LigBuilder are: (1) When the program analyzes the binding pocket of the target protein, it derives the pharmacophore model as a by-product. Such a model could be applied to 3D database searching. (2) User can choose to develop derivatives on a "core" structure (growing strategy) or link several separated groups into an integrated molecule (linking strategy). (3) Molecules are built up by using fragmental building blocks. Various kinds of structure manipulation are provided, such as growing, linking, and mutation. The fragment library is user maintainable. (4) On-the-fly minization of conformation is performed while building the molecules. All the conformations corresponding to energy minima are accepted. (5) Molecules are evolved iteratively by applying Genetic Algorithm. The fitness score of a molecule is evaluated both by its binding affinity with the target protein and its chemical viability. (6) Lipinski rules are applied to screen out molecules which are not "drug- like". Molecules containing any "forbidden" substructure are also rejected. The "forbidden" substructure library is user maintainable. (7) All the input and output molecules are in popular format, i.e. protein in PDB format and ligands in Sybyl Mol2 format. The program is written in C++ and run on UNIX/LINUX workstation. We sincerely invite you to test this program. You can download the program via anonymous FTP to ftp.ipc.pku.edu.cn/pub/software/LigBuilder/. Any feedback will be highly appreciated. And we will make necessary modification on LigBuilder based on your suggestion. With best wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Renxiao Wang Doctoral Candidate _/ _/ Molecular Design Laboratory _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-62751490 Fax: 86-10-62751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/~arthur/arthur.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From chemistry-request@server.ccl.net Thu Apr 29 01:59:37 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA16741 for ; Thu, 29 Apr 1999 01:59:35 -0400 Received: from office.un.md (root@office.un.md [212.0.211.34]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id BAA14948 Thu, 29 Apr 1999 01:56:16 -0400 (EDT) Received: from un.md ([212.0.205.39]) by office.un.md (8.6.13/8.6.12xla) with SMTP id IAA14900 for ; Thu, 29 Apr 1999 08:56:31 +0300 Date: Thu, 29 Apr 1999 08:58:42 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.15) S/N B6042885 Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <14374.990429@mail.ru> To: CHEMISTRY@www.ccl.net Subject: Test molecules for UV-vis spectra calculation Mime-Version: 1.0 Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 8bit +======================---------------- --- -- - - - - . | Hello Chemistry, : . I would like to test available programs for calculation of UV-Vis spectra. I'll use this programs for calculating spectra of organic compounds (ligands), containing cycles and S, O, N hetero-atoms in molecular and ionic forms and complexes of this ligands. Could anybody provide me a references to good enough compounds (and their geometry and spectra) to test this programs? Best regards, Mike mailto:MikePeleah@mail.ru ... Пока толстый сохнет, худой сдохнет . : | . - - - - -- --- ----------------======================+ From chemistry-request@server.ccl.net Thu Apr 29 09:53:17 1999 Received: from rutchem.rutgers.edu (rutchem.rutgers.edu [128.6.1.216]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA21137 for ; Thu, 29 Apr 1999 09:53:17 -0400 Received: from localhost (yong@localhost) by rutchem.rutgers.edu (8.8.8/8.6.10) with SMTP id NAA00918 for ; Thu, 29 Apr 1999 13:49:58 GMT Date: Thu, 29 Apr 1999 09:49:57 -0400 (EDT) From: Dayong He To: chemistry@server.ccl.net In-Reply-To: <199904231015.MAA34812@rs5.thch.unipg.it> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everybody. Do you happen to know where I can find the codes that convert DNA sequence to the corresponding protein sequence or RNA sequence ? Thank you for your information. Regards. Dayong From chemistry-request@server.ccl.net Thu Apr 29 20:17:42 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA27094 for ; Thu, 29 Apr 1999 20:17:42 -0400 Received: from camd.soongsil.ac.kr (camd.soongsil.ac.kr [203.253.24.201]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id UAA18940 Thu, 29 Apr 1999 20:14:11 -0400 (EDT) Received: from camdedu8 (camdedu8.soongsil.ac.kr [203.253.24.213]) by camd.soongsil.ac.kr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id JAA07745 for ; Fri, 30 Apr 1999 09:17:58 +0900 Sender: tblee@camd.soongsil.ac.kr Message-ID: <372990E3.41C6@camd.soongsil.ac.kr> Date: Fri, 30 Apr 1999 21:15:47 +1000 From: Tae Bum Lee Organization: Computer Aided Molecular Design Center X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: ZINDO error message Content-Type: text/plain; charset=euc-kr Content-Transfer-Encoding: 7bit Dear CCLer, I am calculating the Si cluster model using the ZINDO in Cerius2. When I perform the geometry optimization of Si cluster, the last line of output file message is below, -------------------------------------------------------------------------> SENSE LIGHT 2 IS ON (TOO MANY ITERATIONS) MAXIMUM SCF DENSITY DIFFERENCE= 13.564880 FOR ATOM 4 CYCLE 401 E(SCF) = 227.70869926 au DIFF. = -8.85796D+02 COORDINATES ARE MASS WEIGHTED IN STEP IN SEARCH TOO MANY LINE SEARCH STEPS NEEDED WILL USE ALPHA THAT GIVES LOWEST VALUE IF ENERGY WENT DOWN, OTHERWISE WILL TRY STEEPEST DESCENT KSRCH ALPHA ENERGY 1 0.00000000 -583.36346333 2 0.00000000 -357.76837665 3 0.00000000 225.43161539 4 0.00000000 -324.61644853 5 0.00000000 227.70869926 SEARCH JLOW 1 NOTHING MAKES ENERGY GO DOWN End of run. Error code 3 which means: Old error code; no further information ----------------------------------------------------------------------- I don't know the meaning of this message. What is problem? Is it concerned to the spin state or any other SCF option? Any other information will be helpful to me....... -- Tae Bum Lee : Computer Aided Molecular Design Center Tel: 02) 820-0818 Fax : 02) 825-1795 e-mail: tblee@camd.soongsil.ac.kr From chemistry-request@server.ccl.net Fri Apr 30 09:07:42 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA00428 for ; Fri, 30 Apr 1999 09:07:41 -0400 Received: from admin.cnrs-orleans.fr (admin.cnrs-orleans.fr [163.9.1.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA21147 Fri, 30 Apr 1999 09:04:06 -0400 (EDT) Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.8.8/jtpda-5.3) with ESMTP id PAA11953 ; Fri, 30 Apr 1999 15:03:53 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.8.7/8.8.7) id PAA30166; Fri, 30 Apr 1999 15:01:25 +0200 Date: Fri, 30 Apr 1999 15:01:25 +0200 Message-Id: <199904301301.PAA30166@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: mforster@nibsc.ac.uk CC: Gerald.Loeffler@vienna.at, chemistry@www.ccl.net In-reply-to: <37298C17.B38AB66@nibsc.ac.uk> (message from Mark Forster on Fri, 30 Apr 1999 11:55:19 +0100) Subject: Re: CCL:XML for Bioinformtics Data References: <3729775D.C5D6C8BA@vienna.at> <37298C17.B38AB66@nibsc.ac.uk> > XML. Some work in this area has already been done. For more > information on the Biosequence Markup Language (BSML) > see the WWW page of Visual Genomics Inc. at > > http://www.visualgenomics.com/bsml/index.html > > A BSML browser and examples are available for download. And that's not the only one, see for example BioML (http://www.proteometrics.com/BIOML/). It remains to be seen if any proposed DTD will gain acceptance; I wouldn't be surprised if the "first generation" DTDs turned out to be insufficient at a later time. > What is not currently clear to me is whether a given markup language > must to be approved by the WWW consortium, the Math markup > language 1.0 (http://www.w3.org/Math/) has been released as > a W3C recommendation. in April 98; but is this required ? No. You don't even have to tell anyone that you are using a particular DTD (Document Type Definition, i.e. the definition of a particular XML or SGML application). MathML is designed by the W3C, but anyone else can freely use XML for any other purpose. I agree that XML holds a lot of promise for all branches of scientific computing, where people waste incredible amounts of time due to badly designed, undocumented, and incompatible file formats. However, XML only helps, but doesn't guarantee success. Another problem is that XML requires rather sophisticated processing, which makes it improbable that legacy Fortran programs will ever be able to handle it. Newly designed programs can of course profit from existing XML tools and libraries. Even the worst possible XML scenario (lots of similar but incompatible DTDs used in different programs) will be better than the current format chaos, because at least the syntax will be standardized and the semantics can often be guessed reliably. So don't wait, start using XML now! -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Sun May 2 18:58:35 1999 Received: from postoffice.igalaxy.net ([207.126.82.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA29751 for ; Sun, 2 May 1999 18:58:33 -0400 From: kaynjay@igalaxy.net Received: from kaynjay [207.126.85.253] by postoffice.igalaxy.net (SMTPD32-5.01) id A929A30D042E; Sun, 02 May 1999 16:00:57 PDT Date: Sun, 02 May 1999 15:46:50 -0700 To: CCL In-Reply-To: <199904262212.SM00238@kaynjay> Subject: Summary: Rolling H charges into their heavy atoms? X-Mailer: MR/2 Internet Cruiser Edition for OS/2 v1.52 b52 Message-Id: <199905021600.SM00238@kaynjay> I wish to extend my thanks again to those people who replied to my question! Their replies follow my original question below. I greatly appreciate their feedback. Kenward Vaughan In <199904262212.SM00238@kaynjay>, on 04/26/99 at 09:20 PM, kaynjay@igalaxy.net said: >Hello people, >I wanted some opinions from those well versed in the field about a practice >I've seen mentioned in some docking studies with proteins (an area in which >I'm interested). Most PDB files have no H's mapped. Since the ESP is >important in those studies, having some good estimate for the partial >nuclear charges is naturally important. It appears that one can either add >the H's onto the existing structure or take a well-calculated amino acid >structure (using an ab initio program) and additively "roll" the nonpolar H >charges into their respective heavy nuclei. In this case, those which >might H-bond seem to be treated separately (added to the structure), which >makes sense to me. >First, is this a reasonable 1st-level understanding of the approaches to >this? Or have I misunderstood things? >The second approach (rolling charges into the heavy atoms) would certainly >appear to be the easiest to adopt. Is there good reason Not to do either >approach? In both I can see an issue of accuracy for a number of obvious >reasons from the QM perspective, but wonder about the validity of this >concern on the broad scale over which these protein interactions occur. >Any references would also be appreciated. My apologies if this seems >trivial or mundane ... I'm quite new to all of this, and am learning it >near the back of a dark cave ... :) Thanks very much! and the replies: ---------------------------------------------------------------------- From: "R.M.Day" Hi Kenward this might be irrelevant, but your question is far from trivial and is something we fix with MM. XRAY crystallography cannot give you Hydrogen coordinates - hydrogen atoms dont deflect much at all. How this this normally got around is bythe use of MM and with partial charges from dictionaries from the likes of Kollman et al.. These have been found to be "good" enough for most modelling & docking jobs. People have found that such models built this way are pretty well realistic, proven by comparison with NMR etc. Its only a model after all - intuition rules OK. [...] Best of Luck, Richard Day ---------------------------------------------------------------------- From: David van der Spoel Basically, your question boils down to: is it better to add the hydrogens or to use a united atom approach. Obviously the charge is delocalized and therefore it is in principle better to have more particles (the Hs) to be able to reproduce the electronic structure better. The problem is that we do not know the electronic structure of a protein (in a certain conformation) with sufficient accuracy to make a fit of atomic charges that reproduces the electrostatic potential due to the "real" electron density. Thus we use model systems (amino-acid crystal for example) to derive atomic charges, or ab-initio calculations on isolated amino acids. The resulting charges (and the rest of the force field) must then be tested for its ability to reproduce experimental data, and then conclusions on the quality of the charges can be drawn. It should be stated that the trend is towards all-atom force fields, but is not always clear how well they perform. Some (old) references: @Article{Teleman91, author = {O. Teleman and P. Ahlstr{\"o}m and B. J{\"o}nsson}, title = {On the use of united atoms in statistical mechanical simulations of biomolecules}, journal = "Mol. Sim.", year = 1991, volume = 7, pages = {181-194} } @Article{Veenstra92a, author = {D. L. Veenstra and D. M. Ferguson and P. A. Kollman}, title = {How Transferable are Hydrogen Parameters in Molecular Mechanics Calculations?}, journal = "J. Comp. Chem.", year = 1992, volume = 8, pages = {971-978} } @Article{Kini92, author = "R. M. Kini and H. J. Evans", title = "Comparison of Protein Models Minimized by the All-Atom and United Atom Models in the {AMBER} Force Field: Correlation of {RMS} deviation with the Crystallographic {R} Factor and Size", journal = "J. Biomol. Struct. Dyn.", year = "1992", volume = "10", number = "2", pages = "265--279", } @Article{Kaminski94, author = "George Kaminski and Erin M. Duffy and Tooru Matsui and William L. Jorgensen", title = "Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the {OPLS} All-Atom Model", journal = BTjpc, year = "1994", volume = "98", pages = "13077--13082", } Groeten, David. ---------------------------------------------------------------------- >From a later note from Dr. van der Spoel In the united atom models one usually has the polar hydrogens (NH, OH) present while the aliphatic hydrogens (CH) are taken out. These force fields (GROMOS, AMBER, CHARMM, OPLS) usually give reasonable results, but you have to check with the literature yourself. Adding explicit H to aliphatic groups does not seem to make a big difference for proteins (which are dominated by electrostatics) although it does for small organic molecules. Furthermore it is now common in all force fields to have explicit hydrogens on Tyr, Phe and Trp to reproduce quadrupole moments. To get the electrostatic potential you use one of the force field charge sets and a solver for the Poisson Boltzman equation (such as Delphi or MEAD). If you would leave out the dipolar groups and only maintain the charged groups your potential would be correct at long distance but not close to the protein. Actually, what would be interesting I think is to compare the ESP calculated by different charge sets. I have a gut feeling that the results will be fairly similar although the charges sometimes differ quite a lot... Groeten, David. ---------------------------------------------------------------------- From: fleite@thor.biof.ufrj.br Hello Kenward, I'm new at this too. But I was reading and artcile about CHARMM and they talk about the advantages and disadvantages of the extended-atom representation on its third page. The artcile is very big. Here is the reference: Journal of Computational Chemistry, Vol. 4 No. 2, 187-217 (1983). Hope it helps! Best regards, Fernanda ---------------------------------------------------------------------- From: Jeffrey L. Nauss, PhD If I understand you correctly, you are comparing a united atom vs polar hydrogen model vs and all-atom model for molecular structures. >First, is this a reasonable 1st-level understanding of the approaches to >this? Or have I misunderstood things? I would say it is a reasonable start (assuming I understood your point). But "rolling" hydrogens into heavy atoms also includes expanding the Van der Waals radii as well. This accommodates the positions of the hydrogens. >The second approach (rolling charges into the heavy atoms) would certainly >appear to be the easiest to adopt. Is there good reason Not to do either >approach? Early molecular mechanics force fields (Amber and Charmm) were united or polar hydrogen models. The reasons for doing so were many including the lack of computer power 10-20 years ago. Modern force fields (Amber Cornell and Charmm 22) use all atom representations as they are more accurate in terms of intermolecular interactions. However, these modern force fields also work better with explicit solvent. For small molecules, my understanding is that you need an all-atom representation to get any decent results at all. >Any references would also be appreciated. You might try these and references therein: 1. MacKerell Jr., A. D., Wiorkiewicz-Kuczera, J., Karplus, M. 1995. An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117:11946-75 2. Cornell, W. D., Cieplak, P., Bayly, C. L., Gould, I. R., Merz, K. M.,Jr., et al. 1995. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 117:5179-97 3. MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Jr., Evanseck, J. D., et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102:3586-3616 4. Weiner, S. J., Kollman, P. A., Nguyen, D. T., Case, D. A. 1986. An All Atom Force Field for Simulations of Proteins and Nucleic Acids. J. Comp. Chem. 7:230-52 ---------------------------------------------------------------------- And in a later letter from Dr. Nauss ... [...] if you look at Barry Honig's DelPhi, he uses only formal charges on ionizable side chains. He completely ignores partial charges on neutral side chains and the backbone. I have yet to see (or to do myself) comparisons of different charge sets. -- ----------------------------------------------------------- kaynjay@igalaxy.net ----------------------------------------------------------- From chemistry-request@server.ccl.net Sun May 2 19:19:57 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA30133 for ; Sun, 2 May 1999 19:19:56 -0400 Received: from serval.noc.ucla.edu (serval.noc.ucla.edu [169.232.10.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA02608 Sun, 2 May 1999 19:15:47 -0400 (EDT) Received: from indium (Indium.seas.ucla.edu [128.97.83.8]) by serval.noc.ucla.edu (8.9.1a/8.9.1) with SMTP id QAA04636 for ; Sun, 2 May 1999 16:15:13 -0700 (PDT) Message-ID: <001301be94f0$79e894a0$08536180@indium.seas.ucla.edu> From: "Qiang" To: Subject: Molecular Symmetry of G98 Date: Sun, 2 May 1999 16:06:56 -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 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear CCLers, I am trying to use G98 to optimize pentacoordinated Al3H9 with C2 symmetry. However, the linkle died at L202 when the program tried to reorient coordinates. The input file is as follows # RPW91PW91/6-31G Opt Test Al3H9 0 1 Al1 0 0.000 0.000 0.000 Al2 0 0.000 b d Al3 0 0.000 -b d H4 0 0.000 0.000 c H5 0 e1 f1 g1 H6 0 -e1 -f1 g1 H7 0 e2 f2 g2 H8 0 -e2 -f2 g2 H9 0 e3 f3 g3 H10 0 -e3 -f3 g3 H11 0 e4 f4 g4 H12 0 -e4 -f4 g4 Variables: b=2.810 d=0.000 c=1.554 e1=0.000 f1=3.500 g1=1.407 e2=0.000 f2=3.500 g2=-1.407 e3=-0.699 f3=-2.000 g3=0.000 e4=0.479 f4=-1.575 g4=0.000 The end of the output file looks like this: Deg. of freedom 15 Full point group C2 NOp 2 Omega: Change in point group or standard orientation. Error termination via Lnk1e in C:\G98W\l202.exe. Job cpu time: 0 days 0 hours 10 minutes 48.0 seconds. File lengths (MBytes): RWF= 10 Int= 0 D2E= 0 Chk= 7 Scr= 1 This cluster has been calculated by Schaefer et. al [1]. I am trying to repeat their results using Gaussian 98 program. The structure of the cluster is constructed with C2 symmetry in cartesian coordinate. I am wondering whether the failur of calculation is caused by lack of some propriate options related to orbital symmetry. Any suggestion will be a great help to me. Then, I tried to use the keyword "NoSymm" to get the program running, which turns off all the orbital symmetry. I do not know whether the optimized structure is still valid after this. [1] Duke B.J., Liang C., and Schaefer III H.F. J. Am. Chem. Soc. 113 (1991) 2884-2890. Thank you. Qiang UCLA