From owner-chemistry@ccl.net Wed Jul 26 01:24:50 1995 Received: from interramp.com for us005755@interramp.com by www.ccl.net (8.6.10/930601.1506) id BAA12942; Wed, 26 Jul 1995 01:24:16 -0400 Received: from .interramp.com by interramp.com (8.6.10/SMI-4.1.3-PSI-pop-local) id BAA15308; Wed, 26 Jul 1995 01:24:01 -0400 Date: Tue, 25 Jul 95 10:04:39 PDT From: Scott William Chinn Subject: 2D to 3D strux conv: summary To: chemistry@ccl.net X-Mailer: Chameleon - TCP/IP for Windows by NetManage, Inc. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings to all! Thank you for all of your responses! The information was most helpful. Here is a summary: First is the question that I asked and following is the responses. > Date: Wed, 19 Jul 95 02:18:47 PDT > From: Scott William Chinn > Subject: CCL:2D to 3D structure conversion > > I understand that programs such as CONCORD, CORINA and CHEM-X > can convert 2D structures to 3D. > > I have a number of 2D structures which I would like to > convert to 3D and then store in a relational database. > > Is this possible? What does the 3D data look like? I have heard > that CHEM-X will give you something like 400 bitwise operators, > which somehow describe the 3D stucture. Is this correct? Conversion from 2D to 3D is a function offered by several packages (including ours). Basically, a set of relatively simple rules is used to generate 3D geometry, using standard bond lengths and angles. The big problem is that the 2D structure is usually quite different from the desired 3D result; often the 2D structure doesn't have a lot of cues for stereochemistry or overall conformation. You should check the results of such an automated conversion before using them. (After all, even in doing a 3D structural optimization by standard methods one sometimes finds a local minimum that is, by the standards of an intelligent chemist, obviously a poor structure. A 2D --> 3D structure conversion is a still cruder operation.) I don't know relational databases. When HyperChem does a 2D --> 3D conversion, what comes out is a 3D structure: each atom has 3D coordinates and a set of bonds to other atoms. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Scott, It is certainly possible. I have some experience with CONCORD, having used it to convert isomeric SMILES strings to pdb files (there are more choices of input and output formats). The pdb files produced contain the smiles string, the Cartesian coordinates, and a connection table, and can easily be read by humans or other programs. You can view several hundred at http://ibc.wustl.edu/klotho/. If your SMILES string doesn't specify the stereochemistry, CONCORD will try and choose for you. The structures it gets usually accord pretty well with both chemical intuition and crystal structure (see J. Chem. Info CS 33:155-163, 1993), though it does have limitations and does sometimes produce a howler. I have no experience with Corina yet, but from what I hear and read its strengths are complementary to CONCORD's weaknesses and would be a good alternative (please let's not have a flame war). They now have a free email server, and I'm planning to try it out (it's been reported on this list just recently). I have no experience with ChemX. The hardest part may be generating the input for the conversion program; if you think Klotho would be of some assistance to you please let me know. You may be able to find coordinates for your molecules. For example the NCI has its files up on a gopher server, though last time I looked there was no easy way of retrieving a specific molecule. Try the NIH web site, I think there is a pointer from there (sorry I am unable just now to give you the complete address). Data from Cambridge Crystallographic Database are proprietary. I know a number of software vendors sell databases of small molecules in various forms, usually bundled with their software. You may want to give some thought to the types of queries you wish to run: this has a significant impact on choice of database model, organization of the database, and representation of the data. Good luck, Toni Kazic Institute for Biomedical Computing Washington University Scott, > I understand that programs such as CONCORD, CORINA and CHEM-X > can convert 2D structures to 3D. I have used all three of the programs mentioned to convert tens of thousands of structures. They all have their strengths and weaknesses. Chem-X is a database and modeling program that has a 2D-3D converter as one module. The converter is really there for people who don't want to buy a separate conversion program. It has some serious limitations as shipped ( mainly the inability to build large rings ) but has the advantage that the build fragment library is completely open to the user, so fragments can be added or changed. Be aware that unlike the other programs listed above, the Chem-X converter doesn't really attempt to find a good conformation, it expects that you will go on to 3D key the structure and use the replace option to replace the built structure with the best conformation found in the search. If you don't do this step you can have some really bad structures. CONCORD is the oldest of these converters. We have routinely used CONCORD to handle Chem-X build failures and find that it is successful 80-90% of the time ( excluding organometallics ). You might want to look at our WWW page ( http://www.ncifcrf.gov:1994/DTP/dis3d.html ) for some more detailed information on this. We have done some testing with CORINA and think we will end up using it for all our conversions. > I have a number of 2D structures which I would like to > convert to 3D and then store in a relational database. Be aware that CONCORD and CORINA have no database capabilities. If you want to store the 3D structures in an ORACLE database you may want to investigate the program RS3 from PSI. > I have heard > that CHEM-X will give you something like 400 bitwise operators, which > somehow describe the 3D stucture. Is this correct? Like most 3D search programs, Chem-X has a bit screen to do very fast preliminary searches. The bit screen is based on center to center distances. The centers that Chem-X defines are: H-bond donor H-bond acceptor positive charge aromatic center hydrophobic center The five center lead to 15 pairwise distance keys, each with 31 bits representing a certain distance range. There are also 2 keys encoding bond type patterns and 1 key that encodes formula information. The total of 18 keys times 31 bits gives 558 binary descriptors. Hope this helps. DanZ. /************************************************************* ********* * Dan Zaharevitz * Information Technology Branch, Developmental Therapeutics Program * National Cancer Institute * EPN Room 811, 6130 Executive Blvd. Rockville, MD 20892-9903 * email: zaharevitz@dtpax2.ncifcrf.gov phone: (301)496-8747 ************************************************************** ********/ > I have a number of 2D structures which I would like to > convert to 3D and then store in a relational database. > Is this possible? What does the 3D data look like? I have heard > that CHEM-X will give you something like 400 bitwise operators, which > somehow describe the 3D stucture. Is this correct? I assume that you want to search within your database of 3D structures for those compounds which satisfy certain chemical and 3D-geometric specifications. Accomplishing this objective with standard relational database software would be *extremely* awkward and inefficient. Special 3D searching systems (databases and search engines) have been developed specifically for this purpose. Usually, in the course of performing such 3D searches, it is very important to account for the conformational flexibility of the compounds in the database. MDL, Tripos, and Chemical Design Ltd. are the three leading distributors of chemical database software. MDL and Tripos offer the most robust and efficient software, particular with respect to conformational flexibility within the searching process. Tripos software is also tightly interfaced with molecular modeling and analysis software which provides substantial advantage while analyzing the "hits" found from a 3D search. > I understand that programs such as CONCORD, CORINA and CHEM-X > can convert 2D structures to 3D. All three are good converters. The CHEM-X builder generates multiple conformations which are useful only with Chemical Design searching software. In my opinion, this is not the proper approach to handling the conformational flexibility issue. CONCORD and CORINA both generate a single, low-energy structure which the Tripos and MDL searching software "flex" as necessary. For a variety of reasons, CONCORD is, by far, the most widely used and generally accepted 2D to 3D converter. It is distributed by Tripos. Hi Scott, The program, CONVERTER, from Biosym Technologies can also be used to convert 2D Databases to 3D Databases. It accepts as input an MDL sd file of 2D structures (having the input coordinates all zero'ed out is also acceptable) and writes out a corresponding output sd file of 3D structures. One of its interesting capabilities is the ability to automatically recognize chiral centers in your molecule whose chirality is not assigned (via wedge bonds or parity flags in the SD file) and generate multiple output structures corresponding to different chirality assignments to the chiral atoms. A comparison of the program to some other programs appears in: E.M. Ricketts et al, J. Chem. Inf. Comp. Sci., Vol. 33, pp. 905-925 (1993). Regards, Marvin Waldman, Ph.D. Director, Rational Drug Design Biosym Technologies, Inc. e-mail: marvin@biosym.com Dear Scott, we used CONCORD for the 2D/3D conversion of some 200,000 structures which were available in MDL SD-file format. The 3D structures were stored in UNITY from Tripos which we use for 3D searches. It allows to search for 3D atom patterns taking the conformational flexibility into account. It does a good job but UNITY is pretty expensive. The same can be done with the MDL product ISIS-3D. Also not cheap. It is available for VAX, RS-6000 and SGI. We use MDL software in our company, but we have no experience with the current version of ISIS-3D. I don't know whether any of these databases is a relational one. I know that Chemical Design offers a 3D database which allows to store chemical structures. Together with the structure some distance informations are stored as a bit string which basically specifies which distance ranges can be found for various predefined atom groups (e.g. ionic groups, hydrogen bond donors or acceptors etc.). This requires a conformational analysis to be done in advance before the structure is stored in the database. The idea is to make the "on the fly" conformational comparison with a given query structure faster. Both UNITY and ISIS-3D do the same job but store only one conformation and use a fast algorithm for the same purpose. We tested Chemical Design's (CDL) software several years ago and found many problems. However I meanwhile heard that the database tool (not the 2D/3D converter!) from CDL is said to be OK. regards, Herbert -----------Herbert Koeppen, Boehringer Ingelheim KG, Med. Chem. Dept.----------- -----------D-55216 Ingelheim, Germany, e-mail: 100317.2656@compuserve.com-- You can use CORINA to convert your data by an email interface. See http://schiele.organik.uni-erlangen.de/services/3d.html -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- From owner-chemistry@ccl.net Wed Jul 26 02:24:55 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/930601.1506) id CAA13958; Wed, 26 Jul 1995 02:13:14 -0400 From: Received: from rzurs4.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA10677; Wed, 26 Jul 95 08:13:12 +0200 Received: by rzurs4.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA17732; Wed, 26 Jul 1995 08:13:12 +0200 Message-Id: <9507260613.AA17732@rzurs4.unizh.ch> Subject: Problem w/ FTP'd ISIS/Draw To: chemistry@ccl.net Date: Wed, 26 Jul 1995 08:13:11 +0200 (MEST) X-Mailer: ELM [version 2.4 PL24 PGP2] Content-Type: text Content-Length: 874 Dear Colleagues; I recently downloaded ISIS/Draw version 1.2 for Windows from an FTP site: FTP: ftp.demon.co.uk //pub/ibmpc/windows/isis/draw12w.exe When I tried to install in on a PC, the installation proceeded until it reached a file called "reactant.skc", which the computer was unable to open. I downloaded draw12w.exe again from the same site and tried to install it on a different PC, but the same thing happened: the computer was unable to open "reactant.skc". Has anyone else had this or a related experience with the programme draw12w.exe downloaded from the aforementioned FTP site? Is this freeware ver- sion of ISIS/Draw for Windows somehow disabled by the manufacturer? I would appreciate hearing from MDLI in particular on this last point. Thanks in advance to all responders. Sincerely, S. Shapiro ZH toukie@zui.unizh.ch From owner-chemistry@ccl.net Wed Jul 26 06:39:57 1995 Received: from violet.csv.warwick.ac.uk for mailer-daemon@csv.warwick.ac.uk by www.ccl.net (8.6.10/930601.1506) id GAA16660; Wed, 26 Jul 1995 06:33:25 -0400 Message-Id: <14861.199507261033@violet.csv.warwick.ac.uk> Received: from chem.warwick.ac.uk by violet.csv.warwick.ac.uk with SMTP id LAA14861; Wed, 26 Jul 1995 11:33:15 +0100 Received: by chemhp.chem.warwick.ac.uk (1.37.109.4/16.2) id AA20189; Wed, 26 Jul 95 11:49:06 +0100 From: Craig Wilson Subject: Re: CCL:Problem w/ FTP'd ISIS/Draw To: toukie@zui.unizh.ch Date: Wed, 26 Jul 95 11:49:05 BST Cc: CHEMISTRY@ccl.net In-Reply-To: <9507260613.AA17732@rzurs4.unizh.ch>; from "toukie@zui.unizh.ch" at Jul 26, 95 8:13 am Reply-To: msrge@csv.warwick.ac.uk Organization: University of Warwick, COVENTRY, CV4 7AL, England, UK. Telephone: 0203-522187 (International +44 203-522187) Mailer: Elm [revision: 70.85] > > Dear Colleagues; > > I recently downloaded ISIS/Draw version 1.2 for Windows from an FTP site: > > FTP: ftp.demon.co.uk //pub/ibmpc/windows/isis/draw12w.exe > > When I tried to install in on a PC, the installation proceeded until it reached > a file called "reactant.skc", which the computer was unable to open. > > I downloaded draw12w.exe again from the same site and tried to install it > on a different PC, but the same thing happened: the computer was unable to open > "reactant.skc". > > Has anyone else had this or a related experience with the programme > draw12w.exe downloaded from the aforementioned FTP site? Is this freeware ver- > sion of ISIS/Draw for Windows somehow disabled by the manufacturer? I would > appreciate hearing from MDLI in particular on this last point. > > Thanks in advance to all responders. > > > Sincerely, > > S. Shapiro I also expreienced the same problems when I downloaded ISIS. However, I have discovered the solution. After executing draw12w.exe, you MUST run the file INSTALL.BAT ** before ** you run SETUP.EXE. The install file will create various directories, and reactant.skc and all the subsequent .skc files will be found by the setup program. Good luck, Craig -- ******************************************************************************* * Craig Wilson e-mail: msrge@csv.warwick.ac.uk * * Dept. of Chemistry * * University of Warwick * * COVENTRY Phone: 01203-523523 ext. 2541 (UK) * * CV4 7AL * * England, UK. "This isn't a soap opera - it's real life!" * ******************************************************************************* From owner-chemistry@ccl.net Wed Jul 26 08:56:49 1995 Received: from irisdav.chem.vt.edu for rosas@irisdav.chem.vt.edu by www.ccl.net (8.6.10/930601.1506) id IAA18054; Wed, 26 Jul 1995 08:53:32 -0400 Received: by irisdav.chem.vt.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@ccl.net id IAA29023; Wed, 26 Jul 1995 08:50:14 -0400 From: "Victor M. Rosas Garcia" Message-Id: <9507260850.ZM29021@irisdav.chem.vt.edu> Date: Wed, 26 Jul 1995 08:50:10 -0400 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: Failed minimization in MOPAC93 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi CCL'rs, I'm currently minimizing some molecules in MOPAC93, using a dielectric constant of 78.3. Mi starting point is the structure optimized in gas phase using MOPAC 6.0. After the run is finished I get the message: "THE LINE MINIMIZATION FAILED TWICE IN A ROW. TAKE CARE!" And the GRADIENT NORM varies between 2 and 25 (a little too high, I think). This are the keywords I'm using: AM1 EPS=78.3 NOINTER T=3600.00 PRECISE I have looked up in the list of error messages provided in the MOPAC 93 manual but the message is not there. Is this something to be concerned about? Should I be concerned about the gradient norm? Any help will be appreciated. From owner-chemistry@ccl.net Wed Jul 26 09:24:55 1995 Received: from btm2d1.mat.uni-bayreuth.de for wieland@btm2d1.mat.uni-bayreuth.de by www.ccl.net (8.6.10/930601.1506) id JAA18414; Wed, 26 Jul 1995 09:17:09 -0400 From: Received: by btm2d1.mat.uni-bayreuth.de (IBM OS/2 SENDMAIL VERSION 1.3.2)/1.0) id AA0137; Wed, 26 Jul 95 15:14:29 +0200 Message-Id: <9507261314.AA0137@btm2d1.mat.uni-bayreuth.de> Date: Wed, 26 Jul 95 14:58:07 MET To: chemistry@www.ccl.net Subject: Problem w/ FTP'd ISIS/Draw Some time I ago, I also downloaded ISIS Draw for Windows. First I made several tries to get it from the pages http://www.mdli.com (and following). But every time I did so I got corrupt zip-files that sometimes couldn't even be unzipped. After a correspondence with Dr. Osman F. Guner from MDL I tried the British site http://www.ch.ic.ac.uk/ectoc/ectoc.html#downloading which gave me, in the second attempt, correct files. So the problems you have may also result from bad files. Best regards, Th. Wieland PS: I have never figured out why the files got corrupt on the transfer - blame the net?! Thomas Wieland +---------------+ Dipl. Math. |+---- +----+| Lehrstuhl II f. Mathematik |\ \ | || Universitaet Bayreuth | \ \ | || | \ \ | || 95440 Bayreuth | \ \\ || Germany | \ \\ || Tel. +49 (921) 553386 | \ \\ || Fax +49 (921) 553385 | \-------|| +---------------+ From owner-chemistry@ccl.net Wed Jul 26 10:24:59 1995 Received: from PAPALOTL.PQUIM.UNAM.MX for zacarias@PAPALOTL.PQUIM.UNAM.MX by www.ccl.net (8.6.10/930601.1506) id KAA20025; Wed, 26 Jul 1995 10:13:09 -0400 Received: by PAPALOTL.PQUIM.UNAM.MX (931110.SGI/911001.SGI) for chemistry@ccl.net id AA22193; Wed, 26 Jul 95 08:08:37 -0600 From: "Angelica Garcia Zacarias" Message-Id: <9507260808.ZM22191@PAPALOTL.PQUIM.UNAM.MX> Date: Wed, 26 Jul 1995 08:08:35 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Pd cluster parameters Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dear CCL's: Thanks to all who responded to my request for experimental information about Palladium clusters. Unfortunately we did not get what we were looking for. We are performing ab initio calculations on Pd2, Pd3 and Pd4, and we would like to compare our results with experimental information. I would appreciate if someone can send us data (including unpublished ones) or hints about the existence of geometrical parameters or energies (heats of formation, atomization or bond energies). It is surprising to us that the multiplicity of the ground state of the above clusters have not been clearly determined experimentally. On the other hand, the only experimental information on the dissociation energy of Pd2 shows two very separated values, 16.9 and 26.0 kcal/mol. Any comments on this respect are very welcome. Sincerely Angelica Zacarias -- _________________________________________________ Claudia Angelica Garcia Zacarias Quimica Inorganica. Fisica y Quimica Teorica DEPg., Facultad de Quimica, UNAM Mexico, D.F. 04510 Tel/Fax: (525) 622 3724; Tel: (525) 622 3776 e-mail: zacarias@papalotl.pquim.unam.mx zac@servidor.unam.mx _________________________________________________ Solo con nuestras flores nos alegramos Solo con nuestros cantos florece nuestra tristeza Nezahualcoyotl _________________________________________________ From owner-chemistry@ccl.net Wed Jul 26 11:54:59 1995 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.10/930601.1506) id LAA22647; Wed, 26 Jul 1995 11:47:57 -0400 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA25680 (5.65c+CU/IDA-1.4.4/HLK for <@mailhub.cc.columbia.edu:chemistry@ccl.net>); Wed, 26 Jul 1995 11:47:56 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:chemistry@ccl.net id AA04976; Wed, 26 Jul 95 11:48:02 -0400 Date: Wed, 26 Jul 95 11:48:02 -0400 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9507261548.AA04976@still3.chem.columbia.edu> To: chemistry@ccl.net Subject: Announcing the MMIO code library MMIO, the MacroModel Input-Output library, is now available from the CCL archives. MMIO is a tool to read and write MacroModel- format structure files from user applications. It may be freely used and redistributed in commercial or non-commercial codes. It is supplied as source-code with a Makefile and full documentation. The following is a copy of the README file. After this, instructions are given to download MMIO from the CCL archives. ===================================================================== Introduction to the MMIO library Peter S. Shenkin, March, 1995, shenkin@columbia.edu 1. What it is and what it ain't. MMIO stands for "MacroModel Input-Output". The MMIO library is a linkable code library for reading and writing MacroModel structure files. Communication with the calling application is by means of an API (Application Programmers' Interface), a set of function and subroutine calls. Both a C and a Fortran API are provided. The main purpose of MMIO is to insulate the calling application from having to know anything about the actual file format that these files use. For example, we have recently implemented a new, compressed, file format, and we are planning other changes in the future which will either save disk space or increase capabilities. If calling applications use MMIO, they will not have to worry about parsing the new format; the present API will continue to be in force for some time. MMIO does not, however, know anything about chemistry. It is still up to the user application to properly interpret MacroModel atom-types on reading and properly specify them on writing. Similarly, the calling application must properly interpret and specify bond orders. It is possible that in the future we will produce another code library that handles some of these chores; for example, it would contain a function that returns the atomic number, given a MacroModel atom type. 2. Provisions of use. The code is copyrighted; please read the copyright notice that is printed in all code modules. However, you may do nearly anything you wish with MMIO, including incorporating it into a commercial product free of charge. You may also redistribute the source. You may not remove the copyright notice from the source. Also, if you redistribute the source with changes you have made, you must also communicate those changes back to us so that we can redistribute them as well, if we wish to do so. Changes you make for your own proprietary purposes need not be communicated back to us if you do not redistribute source code. Though MMIO works properly as far as we know, and though we will do our best to correct errors or deficiencies as we become aware of them, we do not warrant the correctness of MMIO in any way. Use MMIO at your own risk. 3. Documentation. Two files, README.C and README.Fortran, will be produced when you make the libraries. These describe how to use the libraries and document the API fully. Several code examples are provided. You should study at least one example before using MMIO in your own application. The sample programs are: Fortran API: fmmio.f mmio_uncompress.f C API: cmmio.c mmio_convert.c ( Complicated example -- save for last. ) These programs are heavily commented. 3. Making the libraries and documentation. This is described in the file README.src. The file RCS_version describes the current and past versions of MMIO. If you are considering updating a previous MMIO version, consulting this file will help you decide whether it's worthwhile to do so. 4. Platforms. MMIO is known to run on the following platforms: SGI, IBM, DEC/OSF, HP, FUJITSU It ought to port easily to any UNIX platform. It also ought to port easily to non-UNIX platforms, since it is written entirely in ANSI C, with the exception of some Fortran routines in the Fortran interface, only. ===================================================================== Jan Labanowski was kind enough to provide these explicit instructions for obtaining MMIO (thanks, Jan): > From jkl@ccl.net Wed Jul 26 10:40:07 1995 > You can retrieve the MMIO source library from CCL archives: > > 1) via ftp > ftp www.ccl.net > Name: anonymous > Password: Your_real_e-mail_address > ftp> cd /pub/chemistry/software/SOURCES/C/MacroModel-InpOut > ftp> get mmio_46.txt > ftp> binary > ftp> get mmio.tar.Z > ftp> quit > > 2) via gopher > gopher www.ccl.net 73 > software --> SOURCES --> C --> MacroModel-InpOut > > 3) via Web > http://www.ccl.net/chemistry.html > CCL Archives --> software --> SOURCES --> C --> MacroModel-InpOut > > 4) via e-mail > send a message: > select chemistry > limit 100kBytes > size 50kbytes > help encoders > cd software/SOURCES/C/MacroModel-InpOut > get mmio_46.txt > get mmio.tar.Z > quit > to MAILSERV@www.ccl.net and you will receive text file, and the > uuencoded mmio.tar.Z archive in several parts. You need to splice the > uuencoded parts (remember to delete mail headers) into one file with > an editor. Then uudecode this file and recover the original mmio.tar.Z. > You can then unpack the compressed tar archive on a UNIX machine by > a command: > zcat mmio.tar.Z | tar xvof - Enjoy! -P., and the MacroModel Development Group ***************** Atheist: An evangelical agnostic. ***************** *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* *NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039* ********** World music: What Bluegrass is to a Bulgarian. *********** From owner-chemistry@ccl.net Wed Jul 26 12:11:55 1995 Received: from wugate.wustl.edu for david@wucmd.wustl.edu by www.ccl.net (8.6.10/930601.1506) id MAA23217; Wed, 26 Jul 1995 12:00:16 -0400 Received: from wucmd (wucmd.wustl.edu [128.252.137.1]) by wugate.wustl.edu (8.6.12/8.6.11) with SMTP id LAA18836 for <@wugate.wustl.edu:CHEMISTRY@ccl.net>; Wed, 26 Jul 1995 11:00:15 -0500 Received: by wucmd (931110.SGI/911001.SGI) for @wugate.wustl.edu:CHEMISTRY@ccl.net id AA18820; Wed, 26 Jul 95 09:57:32 -0500 Date: Wed, 26 Jul 1995 09:57:30 -0500 (CDT) From: David Chalmers X-Sender: david@wucmd To: CHEMISTRY@ccl.net Subject: Sulfonamide summary. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello again, Thanks to all who took time to reply to my request for sulfonamide parameters - and there were many. It looks like I missed some obvious ones. Rossi et al. Application of the Free Energy Pertubation Method to Human Carbonic Anhydrase II Inhibitors. J. Med. Chem. 1995, 38, 2061-2069. Nicholas et al., "A Molecular Mechanics Valence Force Field for Sulfonamides Derived by Ab Initio Methods." J. Phys. Chem. 95:9803-9811 (1991). Bindal et al., "Ab Initio Calculations on N-Methylmethansulfonamide and Methyl Methanesulfonate for the Development of Force Field Parameters and Their Use in the Conformational Analysis of Some Novel Estrogens." JACS 112:7861-7868 (1990). These papers report calculations on sulfonamides but no real parameters are given. Vedani, J. Amer. Chem. Soc. 111(1989)4075 (Yeti) Merz, J. Amer. Chem. Soc. 113(1991)4484 (Amber) Various people made additional comments: Quentin McDonald and Peter Shenkin said that the new version of Macromodel contains MM2* sulfonamide parameters developed by Carol Parish and Hanoch Senderowitz. Kent Stewart suggested: There is a nice compilation of aryl sulfonamides in Cambridge Crystal Structure database in the supplementary material in J. Am. Chem. Soc. 117, 1181 (1995). Heather Gordon suggested this paper may be of interest: "Force Field Parameters for Sulfates and Sulfamates based on ab initio calculations: extensions of AMBER and CHARMm Fields" C.J.M. Huige and C. Altona, J. Comput. Chem. 16(1), 56 (1995). David -------------------------------------------------------------------------------- David Chalmers david@wucmd.wustl.edu Department of Mol. Biol. and Pharmacol. Washington University School of Medicine Campus Box 8103, 660 S. Euclid Ave Lab: +1 314 362 2515 St Louis, MO 63110, USA Fax: +1 314 362 7058 ------------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Jul 26 13:10:02 1995 Received: from VMS.HUJI.AC.IL for ALEXK@vms.huji.ac.il by www.ccl.net (8.6.10/930601.1506) id NAA25046; Wed, 26 Jul 1995 13:06:02 -0400 Received: by HUJIVMS (HUyMail-V7b); Wed, 26 Jul 95 20:06:00 +0200 Received: by HUJIVMS (HUyMail-V7b); Wed, 26 Jul 95 17:58:07 +0200 Date: Wed, 26 Jul 95 17:57 +0200 Message-id: <26070095175750@HUJIVMS> From: To: chemistry@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: esff force field HELLO, I am using the 235 version of discover/insight to do calculations on zinc proteins . For these calculations I am using esff force field to setup potentials for zinc, but when I tried to run discover_3 for a zinc protein I could not do it, and I got a message that I can not run discover for a protein that has more than 200 atoms and uses esff force field to setup potentials for zinc. So, if anyone did any calculations (minimization, molecular dynamics) using the esff force and potentials for zinc proteins or any proteins that have more than 200 atoms, please let me know. Also, if you have any comments on the quality of the results from such calculations (references ???) THANK YOU FOR ALL YOUR HELP. Alexandra Kilshtain Dept. of Pharm. Chemistry School of Pharmacy, Hebrew U. of Jerusalem Jerusalem, Israel 91120 Tel: 972-2-757538/9, FAX: 972-2-410740 email: alexk@vms.huji.ac.il From owner-chemistry@ccl.net Wed Jul 26 13:24:59 1995 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by www.ccl.net (8.6.10/930601.1506) id NAA25038; Wed, 26 Jul 1995 13:05:04 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA03703; Wed, 26 Jul 95 10:04:43 -0700 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma003701; Wed Jul 26 10:04:40 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA23158; Wed, 26 Jul 95 10:04:49 -0700 From: "Wayne Huang" Message-Id: <9507261004.ZM23156@mazda.wavefun.com> Date: Wed, 26 Jul 1995 10:04:48 -0700 In-Reply-To: "Angelica Garcia Zacarias" "CCL:Pd cluster parameters" (Jul 26, 8:08am) References: <9507260808.ZM22191@PAPALOTL.PQUIM.UNAM.MX> Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "Angelica Garcia Zacarias" Subject: Re: CCL:Pd cluster parameters Cc: chemistry@ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Regarding your quest for Pd cluster parameters, I have a few comments: We have been developing semiempirical parameters for transition metals for a while. The newly released version of Spartan 4.0 has parameters for 13 d-transition metals now (more to come), which includes Pd parameter. We have tested this module on Pd compounds and the results are promising. For example, I have run geometry optimization on your Pd2. Here is the data: Heat of formation: 171.4 kcal/mol Dissociation Energy: 15.9 kcal/mol (Expt: 16.9 & 26.0 kcal/mol) Pd-Pd distance: 2.508 Ang. I hope this could be of help. --Wayne On Jul 26, 8:08am, Angelica Garcia Zacarias wrote: > Subject: CCL:Pd cluster parameters > Dear CCL's: > > Thanks to all who responded to my request for experimental > information about Palladium clusters. Unfortunately we did > not get what we were looking for. > > We are performing ab initio calculations on Pd2, Pd3 and Pd4, > and we would like to compare our results with experimental > information. > > I would appreciate if someone can send us data (including > unpublished ones) or hints about the existence of geometrical > parameters or energies (heats of formation, atomization or > bond energies). > > It is surprising to us that the multiplicity of the ground > state of the above clusters have not been clearly determined > experimentally. On the other hand, the only experimental > information on the dissociation energy of Pd2 shows two very > separated values, 16.9 and 26.0 kcal/mol. > > Any comments on this respect are very welcome. > > Sincerely > > Angelica Zacarias > -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | /--- ----\ /---/ ---\ ----- /---/ /| / | | Computational Chemist | \ / / / / / / / / / / | / | | Wavefunction, Inc. | \ /---/ /---/ /---/ / /---/ / | / | | huang@wavefun.com |---/ / / / / \ / / / / |/ | +---------------------------------------------------------------------+ | Wavefunction, Inc., 18401 Von Karman, Suite 370, Irvine, Ca 92715 | | Telephone: (714)955-2120 Fax: (714)955-2118 http://wavefun.com | +---------------------------------------------------------------------+ From owner-chemistry@ccl.net Mon Jul 24 16:03:34 1995 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.6.10/930601.1506) id QAA03132; Mon, 24 Jul 1995 16:03:27 -0400 Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA04484 (5.65c/IDA-1.4.4 for ); Mon, 24 Jul 1995 16:05:33 -0400 Received: by zeus.cooper.edu id AA05452 (5.67b/IDA-1.5); Mon, 24 Jul 1995 10:55:50 -0400 From: TOPPER ROBERT Message-Id: <199507241455.AA05452@zeus.cooper.edu> Subject: mass spec prediction: summary To: CHEMISTRY@ccl.net, topper@cooper.edu Date: Mon, 24 Jul 1995 10:55:50 -0400 (EDT) Hi all, here is a summary of responses I got from my inquiry about software to help interpret mass spectra. A summary is given below. Many thanks to those who wrote in with suggestions! In the end, we contacted Trinity Software, who gave us an upgrade from MassSpec 1.0 to MassSpec EXT 3.0.1 for the Macintosh at a very reasonable price. It is a nice program, it runs well under System 7.1 on a Quadra 660AV, and we are quite happy with it. Note however that it lacks the ability to directly interface with programs like ChemDraw and ChemIntosh, so that will probably be a downside as far as some are concerned. However, it is easy to draw structures and the mass-spec options are easily tunable (C13 peaks can be suppressed, cleavage of rings can be suppressed, etc.) Trinity Software can be contacted at 1-800-352-1282. best wishes, robert ************************************************************************ Prof. Robert Q. Topper email: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 School of Engineering WWW: watch this space, coming soon! The Cooper Union FAX: (212) 353-4341 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 USA or the N/R to 8th St/NYU ************************************************************************ The Cooper Union for the Advancement of Science and Art, established by Peter Cooper in 1859, is a private institution of higher learning where all students receive full-tuition scholarships. ************************************************************************ The original posting: Hello all, I'm writing on behalf of a colleague who does quite a bit of mass spectroscopy. He would like to acquire a program which, given a molecular formula, can "predict" the mass spectrum. He'd prefer it if it ran on a Mac, but we also have MS/DOS/Windows and UNIX machines available. Does anyone have any recommendations? We are aware of the existence of MassSpec 3.0 (Trinity Software) for Macintosh, but would welcome any comments on the code's usability, usefulness, etc.. we have a very old version (1.0) of MassSpec, but it doesn't run under system 7 and it's pretty clunky under system 6. ************************************************************************ Responses: >From Jim.Macmillan@uni.edu Wed Jul 12 18:43:40 1995 I bought ChemWindows at the ACS meeting last spring and at the time I got MS Palate. It allows you to take a structure you have drawen with ChemWindows and see the fragments and masses as you bisect the molecule. It is a simple package but useful, I think. I don't do a lot of MS work but it seems to be useful. Jim Macmillan Department of Chemistry University of Northern Iowa macmillan@uni.edu >From MARTIN@cmda.abbott.com Wed Jul 12 18:44:41 1995 ChemIntosh does this I am told. @@@@@@@@@@@ Yvonne Martin, Senior Project Leader @ Computer Assisted Molecular Design Project @@@@@@@@ @ D-47E, AP10 2fl @ @ Abbott Laboratories @ @ 100 Abbott Park Road @@@@@@@@@@ Abbott Park, IL 60064-3500 Phone: 708 937-5362 FAX: 708 937-2625 yvonne.martin@abbott.com >From cye@chem.QueensU.CA Wed Jul 12 19:41:59 1995 I haven't used it but MacSpec (Spire Software) is available through the American Chemican Chemical Society, cat # 2325-4-154. Good luck, Ray Bowers. >From wallyr@netcom.netcom.com Wed Jul 12 20:05:17 1995 I don't do MS, but have heard about a couple of Mac (or Win) programs from SoftShell that might do the trick. They're at 970-242-7502. Wally ======================================================================== Walter E. Reiher III, Ph.D. WallyR@netcom.com Consultant in Computational Chemistry P.O. Box 61056 voice 408-720-0240 Sunnyvale, CA 94088 fax 408-720-0378 From owner-chemistry@ccl.net Tue Jul 25 21:23:40 1995 Received: from merit-mx1.telemail.net for Karl.F.Moschner@urlus.sprint.com by www.ccl.net (8.6.10/930601.1506) id VAA10039; Tue, 25 Jul 1995 21:23:36 -0400 From: X400-Originator: Karl.F.Moschner@urlus.sprint.com X400-Recipients: non-disclosure:; Message-ID: <"Tue Jul 25 18:30:12 199500*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: chemistry@ccl.net, smori@chem.s.u-tokyo.ac.jp Subject: Re: CCL:Converge problem in the optimization on G94 Seiji Mori wrote: I use the gaussian 92 and g94 programs. I have a problem about the geometry optimization and frequency analysis. After the geometry optimization completed ,I performed the frequency calculation analysis. However, from the output of frequency analysis, sometimes Optimization is not completed because values about displacement exceed the thresholds. How should I resolved it and wolud you tell me your thought about this problem ? We have also run into this problem with Gaussian, as well as other ab inito packages, to which the following comments and suggestions by Doug Fox, Gaussian Inc., on this subject are probably applicable: There are several things contributing to your confusion [about optimizations converging only to have successive frequency calculations indicated as not completely converged,] most of them not bugs but rather facts of life. 1) The optimization deals with an approximate Hessian which is updated at each step by looking at the differences in gradients. As the point in question corresponds to a zero gradient in the majority of cases minor errors in this Hessian are of no consequence. 2) For some cases, especially cases with very flat interaction potentials or near zero barriers, when you replace the approximate Hessian with an analytic second derivative the gradient is still converged but the predicted displacement is no longer. If you restart the optimization with Opt=(READFC) after the Freq it will carry on for a cycle or two and converge. Then you can assess the changes. In some cases you can look at the proposed changes before this and see that it is a methyl rotor which has no impact on the chemistry or some such and ignore it. As to tightening up the convergence criteria, this can be helpful if you have seen this behaviour for one or two of a group you are studying and use OPT=TIGHT on the rest. I would not suggest turning this on as default because it will add several cycles to all optimizations, well behaved or not. Another thought which may be useful is to use OPT=LOOSE which will get an approximate structure, run an OPT=CALCFC starting from this structure and then run FREQ at the end. You still have to run two frequencies but the number of steps between the final structure and the CALCFC will be small and fewer errrors will accumulate. 3) The appearance of a second negative (imaginary really) frequency can occur for the above situations, a methyl rotor locked into a maximum with insufficient force to get it free, or it can be a symmetry forbidden mode which is tested by the FREQ. In the former case you can twist the methyl and restart the optimization. In the latter you should consider running an IRC to trace this mode down to the minimum. Also you should display this mode graphically to see what chemistry is involved, Spartan can do this as can Cerius2 from MSI. You can distinguish these cases to some extent based on the symmetry of the mode. If the mode is totally symmetric then it is an artifact and restarting the optimization will fix it. If not you will have to modify the starting structure to break the symmetry to find the true minimum. Doug Fox help@gaussian.com My thanks to Doug Fox for his assistance. _______________________________________________________________________ / \ | Comments are those of the author and not Unilever Research U. S. | | | | Karl F. Moschner, Ph. D. | | | | Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | | 45 River Road Phone: (201) 943-7100 x2629 | | Edgewater, NJ 07020 FAX: (201) 943-5653 | \_______________________________________________________________________/ From owner-chemistry@ccl.net Wed Jul 26 14:55:06 1995 Received: from hsc.usc.edu for masayuki@hsc.usc.edu by www.ccl.net (8.6.10/930601.1506) id OAA29018; Wed, 26 Jul 1995 14:54:50 -0400 Received: (masayuki@localhost) by hsc.usc.edu (8.6.12/8.6.4) id LAA11420 for chemistry@ccl.net; Wed, 26 Jul 1995 11:54:42 -0700 Date: Wed, 26 Jul 95 11:54:39 PDT From: Masayuki Yuki To: chemistry@ccl.net Subject: Summary: HP ftp Problem Message-ID: Dear CCL Subscribers: Here is the summary of responses to my question of ftping large files from HP workstations: I'm not sure this belongs on the CCL, as it is not about chemical software!! Please send it to some group that deals with HP users. You might browse the Web for the HP home page (which I would guess is http://www.hp.com), or for archives of some user group that deals with HP issues. Such a group might be called comp.sys.hp. This site is good for a whole lot of archives: ftp://rtfm.mit.edu/pub/usenet-by-group . Mark Have you looked at the newsgroup comp.sys.hp.hpux? Also, I have been regularly ftp-ing 23MB files from our HP-UX 9.05 system w/out difficulty, so of course it can be made to work. On the other hand, I have documented file corruption on a disk nfs-mounted from one HP to another. (Unfortunately, the system manager does not want to do anything about it.) I assume that you can ftp files of the same size into the SGI from other sources? (Obviously you need to make sure the disk space is there.) A workaround would be to compress the file (if it isn't already) which would bring the size down. Bill Ross Masayuki Yuki masayuki@hsc.usc.edu From owner-chemistry@ccl.net Wed Jul 26 16:55:04 1995 Received: from kodakr.kodak.com for lrbu00@xd88.kodak.com by www.ccl.net (8.6.10/930601.1506) id QAA04313; Wed, 26 Jul 1995 16:40:52 -0400 From: Received: from euler.kodak.com by kodakr.kodak.com with SMTP id AA05163 (5.67b/IDA-1.5 for <@kodakr.kodak.com:chemistry@ccl.net>); Wed, 26 Jul 1995 16:39:44 -0400 Received: from xd88.kodak.com by euler.kodak.com via SMTP (931110.SGI/931108.SGI.ANONFTP) for @kodakr.kodak.com:chemistry@ccl.net id AA21112; Wed, 26 Jul 95 16:40:17 -0400 Received: by xd88.kodak.com (AIX 3.2/UCB 5.64/4.03) id AA12658; Wed, 26 Jul 1995 16:26:17 -0400 Date: Wed, 26 Jul 1995 16:26:17 -0400 Message-Id: <9507261626.ZM14704@xd88.kodak.com> X-Mailer: Z-Mail (3.0.0 15dec93) To: chemistry@ccl.net Subject: solvation in MOPAC93 using COSMO Cc: McKelvey@kodakr.kodak.com Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Netters: On Jul 26, 8:50am, Victor M. Rosas Garcia wrote: > Subject: CCL:Failed minimization in MOPAC93 > Hi CCL'rs, > I'm currently minimizing some molecules in MOPAC93, using a dielectric > constant of 78.3. Mi starting point is the structure optimized in gas phase > using MOPAC 6.0. After the run is finished I get the message: > > "THE LINE MINIMIZATION FAILED TWICE IN A ROW. TAKE CARE!" > > And the GRADIENT NORM varies between 2 and 25 (a little too high, I think). > > This are the keywords I'm using: > > AM1 EPS=78.3 NOINTER T=3600.00 PRECISE > > I have looked up in the list of error messages provided in the MOPAC 93 manual > but the message is not there. Is this something to be concerned about? Should > I be concerned about the gradient norm? > > Any help will be appreciated. > Observations: Using the solvent model, COSMO, in Mopac93 is requires a bit of adjustment in thinking. After hundreds of runs using it I have found that the gradient does not settle down nearly as fast st the heat of formation. Thus, I have modified my code to stop after the average deviation value of the heat of formation over the last 5 geometry cycles is less than 0.01 Kcal. Usually I find that further grinding gains nothing but lost computer time. Further I always use the EF optimiser. Lastly, I have modified the program to test the sign of the input dielectric constant; if it is negative then a gas phase optimisation is run first, and then the solvated run is begun using the gas phase geometry, gas phase Hessian, and the gas phase density to start the solvated optimisation. This trouble helps tremendously. The optimisation gets as far as it is going to go quicker. Hope this helps. Regards, John McKelvey -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 -- From owner-chemistry@ccl.net Wed Jul 26 17:55:05 1995 Received: from nih-csl.dcrt.nih.gov for gmercier@helix.nih.gov by www.ccl.net (8.6.10/930601.1506) id RAA05620; Wed, 26 Jul 1995 17:50:14 -0400 Received: from [128.231.66.71] (ppc71.od.nih.gov) by nih-csl.dcrt.nih.gov (4.1/1.35(alw-2.4)) id AA04526; Wed, 26 Jul 95 17:50:10 EDT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 Jul 1995 17:57:11 -0500 To: chemistry@ccl.net From: gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.) Subject: Gd gaussian basis set for dft? Hi! I need help locating a gaussian basis set for dft computations using Gd (Gadolinium) or other lanthanides. Ideally, I would prefered a basis with effective core potentials that incorporate some of the relativistic corrections. I tried the ccl archives, and even the EMSL web site without success. I remember that the developers of dgauss apparently have developed some bs for the entire periodic table, and that this was supposed to be available through the net. I have been unsuccessful in getting to their site through infoseek and netscape. Any help would be appreciated! Sincerely, Gustavo A. Mercier, Jr. M.D.-Ph.D. NIH - LDRR OD OIR LDRR Building 10 Room B1N256 10 Center Dr MSC 1074 Bethesda, Maryland 20892-1074 phone: 301-402-3586, 301-496-1981 fax: 301-402-3216 e-mail: gmercier@helix.nih.gov From owner-chemistry@ccl.net Wed Jul 26 19:55:05 1995 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by www.ccl.net (8.6.10/930601.1506) id TAA06712; Wed, 26 Jul 1995 19:46:03 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA04448; Wed, 26 Jul 95 16:45:45 -0700 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma004446; Wed Jul 26 16:45:15 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA05960; Wed, 26 Jul 95 16:45:25 -0700 From: "Wayne Huang" Message-Id: <9507261645.ZM5958@mazda.wavefun.com> Date: Wed, 26 Jul 1995 16:45:24 -0700 In-Reply-To: gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.) "CCL:Gd gaussian basis set for dft?" (Jul 26, 5:57pm) References: Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.) Subject: Re: CCL:Gd gaussian basis set for dft? Cc: chemistry@ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Jul 26, 5:57pm, Gustavo A. Mercier, Jr. wrote: > Subject: CCL:Gd gaussian basis set for dft? > Hi! > > I need help locating a gaussian basis set for dft computations using > Gd (Gadolinium) or other lanthanides. Ideally, I would prefered a > basis with effective core potentials that incorporate some of the > relativistic corrections. > > I tried the ccl archives, and even the EMSL web site without success. > > I remember that the developers of dgauss apparently have developed > some bs for the entire periodic table, and that this was supposed to > be available through the net. I have been unsuccessful in getting to > their site through infoseek and netscape. > > Any help would be appreciated! > > Sincerely, > > > Gustavo A. Mercier, Jr. M.D.-Ph.D. > NIH - LDRR > OD OIR LDRR > Building 10 Room B1N256 > 10 Center Dr MSC 1074 > Bethesda, Maryland 20892-1074 > phone: 301-402-3586, 301-496-1981 > fax: 301-402-3216 > e-mail: gmercier@helix.nih.gov In case you might be interested, we are currently developing semiempirical parameter for Gadolinium, sampling all from large (quantum mechanically) molecules and expecting to be available very soon (next month). I will be interested to see summary of your quest. --Wayne -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | /--- ----\ /---/ ---\ ----- /---/ /| / | | Computational Chemist | \ / / / / / / / / / / | / | | Wavefunction, Inc. | \ /---/ /---/ /---/ / /---/ / | / | | huang@wavefun.com |---/ / / / / \ / / / / |/ | +---------------------------------------------------------------------+ | Wavefunction, Inc., 18401 Von Karman, Suite 370, Irvine, Ca 92715 | | Telephone: (714)955-2120 Fax: (714)955-2118 http://wavefun.com | +---------------------------------------------------------------------+