From ldw@pchsgi25.IPC.PKU.EDU.CN Thu Mar 16 03:12:54 1995 Received: from pchsgi25.IPC.PKU.EDU.CN for ldw@pchsgi25.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/930601.1506) id CAA14863; Thu, 16 Mar 1995 02:59:22 -0500 Received: by pchsgi25.IPC.PKU.EDU.CN (911016.SGI/911001.SGI) for chemistry@ccl.net id AA04123; Thu, 16 Mar 95 07:56:25 GMT Date: Thu, 16 Mar 1995 15:56:23 +0800 (SST) From: Lin Dawei X-Sender: ldw@pchsgi25.IPC.PKU.EDU.CN To: chemistry@ccl.net Subject: Where can I get the Document of Dmol program? In-Reply-To: <9503131627.AA16650@alf.biochem.mpg.de> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netter, Dmol is quantum chemistry calculation program using the density function method. Who can kindly tell me where can I find the Document of how to use it. Thanks in advance, Dawei -------------------------------------------------------------------- ''*'''*'''*'''*'''*'''*'''*'''*'''*'''*'''*'''*'''*'''*'''*'''*'''*' '***'***'***'***'***'***'***'***'***'***'***'***'***'***'***'***'*** ''|'''|'''|'''|'''|'''|'''|'''|'''|'''|'''|'''|'''|'''|'''|'''|'''|' -------------------------------------------------------------------- Dawei LIN Ph.D student of Institute of Physical Chemistry Chemistry Department Peking University ldw@pchindigo2.ipc.pku.edu.cn Beijing 100871 Telephone (861)-2501490 P.R.China Fax (861)-2501725 -------------------------------------------------------------------- From hinsenk@ERE.UMontreal.CA Thu Mar 16 10:13:07 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/930601.1506) id KAA20204; Thu, 16 Mar 1995 10:06:18 -0500 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA15318 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Thu, 16 Mar 1995 10:03:21 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA00745; Thu, 16 Mar 95 10:03:19 -0500 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA03540; Thu, 16 Mar 95 10:03:19 -0500 Date: Thu, 16 Mar 95 10:03:19 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9503161503.AA03540@cyclone.ERE.UMontreal.CA> To: mrigank@imtech.ernet.in Cc: chemistry@ccl.net In-Reply-To: <9503151632.AA13629@doe.ernet.in> (message from Mrigank on Tue, 14 Mar 95 10:36:19 +0530) Subject: Re: CCL:malloc etc. on DEC Alpha I am finding in using 'malloc' family or routines[malloc, free etc.] on our DEC alpha machines running OSF/1. whenever they are called the program gives segmentaion fault or memory fault and aborts. The code works very fine on other machines. These are veru eesential in many huge comp. chem programs where memory need to allocated as needed rather than fixed arrays and i can not change the developed code for it is pain as well as not usefull. There might be a bug in DEC's version of malloc(), but that is highly improbable - malloc() is a very fundamental routine for many Unix programs, and quite old, so bugs should have been found long ago. You might try to link with the compiler option -lmalloc (available on many Unix machines, but I am not sure about the Alphas), which simply replaces malloc() by a different version, optimized for speed rather than memory space. However, in all cases of malloc()-related crashes I have experienced so far (and that is a large number), the code calling malloc() was at fault. The most typical bug is memory access beyond the allocated space. Some versions of malloc() are quite forgiving if only a few more bytes are used, which is often the case, and this explains why such programs work on some machines but not on others. Another common way to ruin malloc's data space is to work with undefined addresses (bad pointers in C, or wrong number of subroutine parameters in Fortran). My recommendation is not to use programs that crash in malloc(). Even if they work on some machines, they are essentially buggy and not to be trusted - even if they don't crash they might produce wrong results. I know that often nothing else is available, but in my opinion an unreliable program is no better than no program at all. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From winnpx@postman.essex.ac.uk Thu Mar 16 11:12:55 1995 Received: from postman.essex.ac.uk for winnpx@postman.essex.ac.uk by www.ccl.net (8.6.10/930601.1506) id LAA21696; Thu, 16 Mar 1995 11:09:46 -0500 Received: from postman.essex.ac.uk by postman.essex.ac.uk with SMTP (PP) id <27034-0@postman.essex.ac.uk>; Thu, 16 Mar 1995 16:09:26 +0000 From: Winn P J Date: Thu, 16 Mar 95 16:09:22 GMT Message-Id: <8753.9503161609@solb1.essex.ac.uk> To: chemistry Subject: BSSE (Quantum ab initio). What is the current consensus on the affect of basis set superposition errors on ab initio quantum calculations???? In particular I would be interested in:- (i) The affect it has on interatomic distances when optimising a group of molecules. (ii) The overall expected error in interaction energies one might expect from a group of optimised molecules. (iii) Identifying you have a BSSE (iv) Correcting for BSSE. (v) A reference covering the above problems in a consistent manner. I have found many references that deal with BSSE but nothing that really gives an overview of the whole problem. All help is gratefully received, no matter how small. Peter Winn. winnpx@essex.ac.uk From bruce@cosy.utmb.edu Thu Mar 16 11:15:35 1995 Received: from cosy.utmb.edu for bruce@cosy.utmb.edu by www.ccl.net (8.6.10/930601.1506) id KAA21081; Thu, 16 Mar 1995 10:41:09 -0500 Received: by cosy.utmb.edu (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@ccl.net id AA00390; Thu, 16 Mar 95 09:45:57 -0600 From: "Bruce A. Luxon" Message-Id: <9503160945.ZM388@cosy.utmb.edu> Date: Thu, 16 Mar 1995 09:45:50 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: Coordinate Fitting Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 CCL Readers, We've used David Heisterberg's (at OSC) QUATFIT for several years with good results. However, we don't routinely use coordinates in the XYZ (XMOL) format so when we want to use QUATFIT we need to do several format translations (for which BABEL by Pat Walters at U. AZ has been invaluable). We use AMBER for the most part so "PDB-like" coordinate files are the norm in our work. These also contain more information than XYZ files - a feature we like, too. My question is: Is there a high quality UNIX (SGI) coordinate fitting routine available that is more PDB oriented than QUATFIT? Thanks in advance for your replies, Bruce -- *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon, Ph.D * * Assistant Professor * * UTMB NMR Center U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* From elewars@alchemy.chem.utoronto.ca Thu Mar 16 12:13:01 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/930601.1506) id MAA23819; Thu, 16 Mar 1995 12:12:16 -0500 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.10/8.6.10) id MAA29898 for chemistry@ccl.net; Thu, 16 Mar 1995 12:12:04 -0500 Date: Thu, 16 Mar 1995 12:12:04 -0500 From: "E. Lewars" Message-Id: <199503161712.MAA29898@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: PROBLEM WITH A PES SCAN Dear Netters: Can anyone see why the Gaussian 92 job (1) below fails while (2) works? Thanks E. Lewars Doesn't work: (1) # am1 Scan Potential surface scan on H2O; O2H1:initial+10 values; A321:initial+10 values. 11 H3O1, 11 A312 values: 121 points. HOH angle=2(A312),90-->190; HO .95--> 1.05 0 1 O1 X2 O1 1. H3 O1 H3O1 X2 A312 H4 O1 H3O1 X2 A312 H3 180. H3O1 0.95 10 0.01 A312 45.0 10 5.0 --------------------------- tail end of output: . . . . Z-Matrix orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 8 .000000 .000000 .000000 2 -1 .000000 .000000 1.000000 3 1 .950000 .000000 .000000 4 1 -.950000 .000000 .000000 ---------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 1 O .000000 2 X 1.000000 .000000 3 H .950000 1.379311 .000000 4 H .950000 1.379311 1.900000 .000000 Interatomic angles: X2-O1-H3= 90. X2-O1-H4= 90. H3-O1-H4=180. STOICHIOMETRY H2O FRAMEWORK GROUP D*H[O(O),C*(H.H)] DEG. OF FREEDOM 1 FULL POINT GROUP D*H NOP 8 0Omega: Change in point group or standard orientation. Error termination in Lnk1e. Signal 11: segmentation violation PROCEDURE TRACEBACK: ( 0) 0x80b9fdf0 a_c_t + 0x84 [/usr/lib/pa1.1/libcl.sl] ( 1) 0x0002e38c HPPAC_ldiv + 0x7f46ad24 [/usr/lib/pa1.1/libcl.sl] ( 2) 0x400363a0 blas_$$dgemm_pcxt + 0x3fff57e8 [/g92/l202.exe] Stack_Trace: error while unwinding stack -------------------------------------------------- Works: (2) # am1 Scan Potential surface scan on H2O; 2 HO steps of .05 each 2 A312 steps of 25 each; HOH angle=2(A312), 90-->190. 3X3=9 points 0 1 O1 X2 O1 1. H3 O1 H3O1 X2 A312 H4 O1 H3O1 X2 A312 H3 180. H3O1 0.95 2 0.05 A312 45.0 2 25.0 From S.R.Kilvington@soton.ac.uk Thu Mar 16 13:13:02 1995 Received: from beech.soton.ac.uk for S.R.Kilvington@soton.ac.uk by www.ccl.net (8.6.10/930601.1506) id NAA25523; Thu, 16 Mar 1995 13:12:46 -0500 Received: from vision.soton.ac.uk (vision.soton.ac.uk [152.78.128.74]) by beech.soton.ac.uk (8.6.10/hub-8.5) with ESMTP id SAA05007 for ; Thu, 16 Mar 1995 18:12:29 GMT Received: (from srk@localhost) by vision.soton.ac.uk (8.6.10/client-8.6) id SAA27313 for chemistry@ccl.net; Thu, 16 Mar 1995 18:13:50 GMT Message-Id: <199503161813.SAA27313@vision.soton.ac.uk> Subject: CCL:malloc etc. on DEC Alpha To: chemistry@ccl.net Date: Thu, 16 Mar 1995 18:13:49 +0000 (GMT) From: "Simon Kilvington" X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1260 Konrad Hinsen wrote: > > However, in all cases of malloc()-related crashes I have experienced > so far (and that is a large number), the code calling malloc() was at > fault. The most typical bug is memory access beyond the allocated space. > Some versions of malloc() are quite forgiving if only a few more > bytes are used, which is often the case, and this explains why such > programs work on some machines but not on others. Another common > way to ruin malloc's data space is to work with undefined addresses > (bad pointers in C, or wrong number of subroutine parameters in Fortran). > a (fairly) easy way to check for writing passed the end of malloc blocks is to replace calls to malloc with calls to a routine which claims slightly more space than is needed, puts some id characters at the start and end of the block eg "MALLOC_BLOCK" or something, and returns a ptr to the first byte after the id. Then replace calls to "free" with a routine that first checks whether the id characters are still intact. If they have changed something has writen before/after the start/end of the block. hope this helps, Si. --- Simon Kilvington, srk@soton.ac.uk PS: make sure your id is a multiple of 4 (8?) bytes or you may get some alignment problems. From cassee@voeding.TNO.NL Thu Mar 16 14:13:04 1995 Received: from hearnvax.nic.surfnet.nl for cassee@voeding.TNO.NL by www.ccl.net (8.6.10/930601.1506) id NAA25919; Thu, 16 Mar 1995 13:20:15 -0500 Received: from frontier (frontier.tno.nl) by HEARNVAX.nic.SURFnet.nl (PMDF V4.2-12 #3330) id <01HO7JUC5RXC00GZHN@HEARNVAX.nic.SURFnet.nl>; Thu, 16 Mar 1995 16:00:15 +0100 (MET) Received: from hvva01.voeding.tno.nl by frontier (4.1/1.53) id AA15363; Thu, 16 Mar 95 15:57:34 +0100 Received: from HVVC03 (HVVC03::MAILER) by HVVA01 (MX V4.1 AXP) with SMTP (DECnet); Thu, 16 Mar 1995 15:57:49 EST Received: by hvvc03.voeding.tno.nl (MX V4.1 VAX) id 3; Thu, 16 Mar 1995 15:55:27 EST Date: Thu, 16 Mar 1995 15:55:16 -0500 (EST) From: "FLEMMING CASSEE,ZEIST, THE NETHERLANDS" Subject: model for 3 compound competitive interaction Sender: cassee@voeding.TNO.NL To: CHEMCOM@UBVM.CC.BUFFALO.EDU, CHEMED-L@UWF.CC.UWF.EDU, CHEMISTRY@ccl.net Message-id: <0098D73E.CC7FEE20.3@hvvc03.voeding.tno.nl> X-Envelope-to: CHEMISTRY@ccl.net Content-transfer-encoding: 7BIT I am not sure wether this is the appropriate place to ask my question, but I'll try... >From the Michaelsi-Menten equations we know that enzyme activities can be decribed when one know the maximum activity and the affinity constant for a given substrate.This model can in general be applied to receptor- mediated effects. Competitive interaction for a receptor can be described by the equation: Ea,b = Ea,max*Kb*[a] + Eb,max*Ka*[b]/(Ka*kb+kb*[a]+ka*[b]) in whcih E is the effect, Ea,max the max. effect, [a] and [b] the concentrations of each compound and K (or k) the affinity constants fro compound a or b. However, we like to describe the competitive interaction for three compounds. Who can help me finding the equation for three-compound interactions?? I am not a member of this list, so please send your answer to: cassee@tno.voeding.tno Thanks! Flemming --------------------------------------------------------------------- Flemming R. Cassee tel: +31 3404 44537 Division of Toxicology fax: +31 3404 60264 TNO Nutrition and Food Research Institute cassee@voeding.tno.nl --------------------------------------------------------------------- From jxh@ibm12.biosym.com Thu Mar 16 14:22:38 1995 Received: from bioc1.biosym.com for jxh@ibm12.biosym.com by www.ccl.net (8.6.10/930601.1506) id OAA26878; Thu, 16 Mar 1995 14:08:27 -0500 Received: from ibm12.biosym.com by bioc1.biosym.com (5.64/0.0) id AA22892; Thu, 16 Mar 95 11:08:47 -0800 Received: by ibm12.biosym.com (AIX 3.2/UCB 5.64/4.03) id AA12884; Thu, 16 Mar 1995 11:08:46 -0800 Received: from Messages.8.5.N.CUILIB.3.45.SNAP.NOT.LINKED.ibm12.biosym.com.rs.aix3 via MS.5.6.ibm12.biosym.com.rs_aix3; Thu, 16 Mar 1995 11:08:45 -0800 (PST) Message-Id: Date: Thu, 16 Mar 1995 11:08:45 -0800 (PST) From: Joerg Hill Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable To: CHEMISTRY@ccl.net Subject: Re: CCL:BSSE (Quantum ab initio) Peter Winn asks: > What is the current consensus on the affect of > basis set superposition errors on ab initio quantum = > calculations???? In particular I would be interested > in:- > = > (i) The affect it has on interatomic distances when > optimising a group of molecules. > = > (ii) The overall expected error in interaction = > energies one might expect from a group of optimised > molecules. > = > (iii) Identifying you have a BSSE > = > (iv) Correcting for BSSE. > = > (v) A reference covering the above problems in a consistent manner. > = > I have found many references that deal with BSSE > but nothing that really gives an overview of the > whole problem. The BSSE is always present if you are doing calculations on intermolecula= r interactions. In this case you will do a calculation on your molecules al= one (monomers) and then you will put these molecules together (complex, super= molecule approach) and do another calculation. From the results of all these calcu= lations you will try to figure out what happens when the molecules interact. Unfo= rtunately, by putting all molecules together, you add additional basis functions to = your monomers (the basis functions of the other monomers), so that your basis = set becomes more flexible (and the energy therefore lower) compared to your m= onomer calculations. Or, to put it another way, the electrons in your monomer ar= e described by basis functions of the other monomers. Therefore, your BSSE depends on the quality (size) of your basis set. If you use a larger basi= s set, your electrons will be described more complete in the monomer basis,= thus reducing the BSSE. Since the BSSE affects the energy it will affect all properties calculate= d: interaction energies, the geometry changes going from monomers to the com= plex etc. The standard method of correcting for the BSSE is the counterpoise correction method of Boys and Bernardi (S.F. Boys, F. Bernardi; Mol. Phys= . 19, 553 (1970)). This method requires additional calculations to be performed= for the monomers: You take the basis functions as they are in the complex, bu= t remove all the atoms which do not belong to your monomer (creating so-cal= led ghost functions). Then you do a calculation for your monomer with this la= rger basis set. Your BSSE for the interaction energy is then: BSSE =3D (E(a)-E(a*)) + (E(b)-E(b*)) = (1) where E(a) and E(b) are the energies of the monomers without ghost functi= ons and E(a*) and E(b*) are the energies of the monomers with ghost functions= . (Note: This procedure in ambigious if you have more than two molecules; L. Turi, J. J. Dannenberg; J. Phys. Chem. 97, 2488 (1993).) The number yo= u get from Eq. (1) tells you something about the quality of your basis set.= It should be significantly smaller than the effect you are looking at (ca= n be hard to achieve). If you are using a correlated method you will see a much larger BSSE with the same basis set compared to SCF. This has to do with having additional virtual orbitals in the complex (S. Saeb=F8, W.= Tong, P. Pulay; J. Chem. Phys., 98, 2170 (1993)). As mentioned above, the BSSE also affects the geometry. I haven't seen an= y paper which has done a BSSE correction for geometries. In principle you have to do the same correction at each step of your geometry optimization= calculating the gradient from the corrected energy. The counterpoise correction also does not recover all of the BSSE, since it does not allow the ghost functions to change their positions in space.= There are a lot of references for the BSSE (from a previous discussion of this topic on the CCL, you may look in the CCL archives for more): - "Gaussian Basis sets for Molecular Calculations", S. Huzinaga, Elsevier= (1991) - "Ab Initio Calculations", P. Carsky and M. Urban, Springer- Verlag, Lecture Notes in Chemistry, 1980. - "Intermolecular Complexes", P. Hobza and R. Zahradnik, Academia, Prague= (1988) Joerg-R. Hill -------------------------------------------------------------------------= ------- Dr. Joerg-Ruediger Hill | Every attempt to employ mathematical methods = in the Biosym Technologies, Inc. | study of chemical questions must be considere= d pro- 9685 Scranton Road | foundly irrational and contrary to the spi= rit of San Diego, CA 92121-2777 | chemistry ... If mathematical analysis shoul= d ever USA | hold a prominent place in chemistry - an aber= ration | which is happily almost impossible - it= would Phone (619) 546-5508 | occasion a rapid and widespread degenerat= ion of Fax (619) 458-0136 | that science. E-mail jxh@biosym.com | A. Comte= , 1830 -------------------------------------------------------------------------= ------- The opinions expressed in this message are my personal opinions and no o= ffical statements of Biosym Technologies, Inc. For informations about Biosym pr= oducts send mail to: rcenter@biosym.com. -------------------------------------------------------------------------= ------- From jstevens@tessa.iaf.uiowa.edu Thu Mar 16 15:13:02 1995 Received: from ns-mx.uiowa.edu for jstevens@tessa.iaf.uiowa.edu by www.ccl.net (8.6.10/930601.1506) id OAA27554; Thu, 16 Mar 1995 14:33:23 -0500 Received: from tessa.iaf.uiowa.edu by ns-mx.uiowa.edu (8.6.10/19950309.1) on Thu, 16 Mar 1995 13:33:21 -0600 id NAA25175 with SMTP Received: by tessa.iaf.uiowa.edu (920330.SGI/891024) on Thu, 16 Mar 95 13:31:08 -0600 id AA22027 Date: Thu, 16 Mar 1995 13:30:31 -0600 (CST) From: jws Subject: knowledge based protein modeling (fwd) To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To all protein modelers, Is it possible to generate a very crude model for a small protein (95 aa) if you know the following: hydrophobic/hydrophilic regions, antibody binding epitopes, carbohydrate linkage sites, and disulfide linkages? If this is possible could you provide me with some references and what programs are being used. I currently have access to most modules for sybyl 6.10 which are running on various SGI platforms. I know that homology modeling is possible using "composer", "homology", etc., but in this case there are no related or homologous (based 20 % homology cut-off). We don't need an "acurate" model, rather a very crude "first" approximation which should provide us with the gross anatomy of the protein. Thanks, Michelle P.S. my e-mail address is jstevens@tessa.iaf.uiowa.edu From hinsenk@ERE.UMontreal.CA Thu Mar 16 15:17:57 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/930601.1506) id OAA27497; Thu, 16 Mar 1995 14:31:31 -0500 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA03244 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Thu, 16 Mar 1995 14:28:51 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA03645; Thu, 16 Mar 95 14:28:49 -0500 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA08001; Thu, 16 Mar 95 14:28:49 -0500 Date: Thu, 16 Mar 95 14:28:49 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9503161928.AA08001@cyclone.ERE.UMontreal.CA> To: chemistry@ccl.net In-Reply-To: (message from Charles Letner on Thu, 16 Mar 1995 12:50:25 -0800 (PST)) Subject: Re: CCL:malloc etc. on DEC Alpha > My recommendation is not to use programs that crash in malloc(). > Even if they work on some machines, they are essentially buggy > and not to be trusted - even if they don't crash they might > produce wrong results. I know that often nothing else is > available, but in my opinion an unreliable program is no better > than no program at all. Your point is well taken, but... Don't most programs have some bugs here and there? I've seen very few programs that didn't have some kind of bug including OS's. It is true that most non-trivial programs have bugs somewhere, but there are enormous differences in their number and severity. As has been pointed out by Simon Kilvington, it is quite easy to check for writing past the end of malloc blocks (unless this occurs extremely rarely, of course). So if a program shows crashes of this kind, you may assume that its author has *not* done this simple test. For me that is reason enough not to use such programs. Unfortunately, many programmers (especially among scientists) still think that it is sufficient to run a few test cases to validate their programs. What one should do, and what many people in other fields are already doing, is to think about debugging from the beginning of the design process. Whenever your start to write a piece of code, your first thought should be "How can I check whether I have made a mistake?" Every program unit should be able to test the validity of its input arguments; if this is expensive, use conditional compilation to remove the tests from production code. Choose variable and function names that are sufficiently different from one another that typos can be caught by the compiler. Use all available tools for checking your code (ftncheck for Fortran, lint for C), and make use of all compiler options that help in debugging (i.e. -C with f77). I could extend this list, but all this has been published before. Whoever really wants to write reliable code can do so with little effort. For some reasons that I cannot follow, scientists seem to ignore the considerable progress that has been made in software engineering during the last decades. Even big and much-used packages are in such a bad shape that they seem to have been written by first-year students as a programming exercise. I have heard excuses such as "I don't have time to learn about programming techniques", but the people saying that seem to have enough time to waste it on endless debugging and on running programs whose results cannot be trusted. I have been working in commercial software development (non- scientific) for more than a decade, and I am sure my company would have been out of business long out if it had this "scientific" attitude towards software development. Now I will sit back and wait for the well-deserved flames... ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From berkley@wubs.wustl.edu Thu Mar 16 15:24:35 1995 Received: from ecl.wustl.edu for berkley@wubs.wustl.edu by www.ccl.net (8.6.10/930601.1506) id OAA27105; Thu, 16 Mar 1995 14:21:33 -0500 Received: from wubs.wustl.edu by ecl.wustl.edu (5.0/ECL-A1.27) id AA10946; Thu, 16 Mar 1995 13:21:31 -0600 Received: by wubs.wustl.edu; (5.65/1.1.8.2/26Aug94-0755AM) id AA05333; Thu, 16 Mar 1995 13:21:25 -0600 Date: Thu, 16 Mar 1995 13:21:25 -0600 From: "Mr. Berkley Shands" Message-Id: <9503161921.AA05333@wubs.wustl.edu> To: chemistry@ccl.net Subject: malloc etc. on DEC Alpha content-length: 11062 It has been my observation that most of the malloc errors are array overruns/underruns. If you have not used 64 bits machines before, start by watching your pointers. here is a snippet of code to do memory management as suggested by Simon Kilvington, srk@soton.ac.uk..... No warranty expressed, implied, desired, or flames needed. /* con_memory.c malloc/free shells and common error reporting */ /*@ process system supplied include files @*/ #include #include #include #include #include #include /*@@*/ /*@ process local include files @*/ /* Some useful prototypes */ #define MODULE #define PROTOTYPE #define local static #define FALSE 0 PROTOTYPE char *mem_alloc (int, int, char *); PROTOTYPE void mem_free (void *, int, char *); PROTOTYPE char *mem_realloc (void *, int, int, char *); #define MEM_ALLOC(i) mem_alloc (i, __LINE__, __FILE__) #define MEM_FREE(i) mem_free (i, __LINE__, __FILE__) #define MEM_REALLOC(i,j) mem_realloc (i, j, __LINE__, __FILE__) /*@@*/ /*@ define symbolic parameters for table and debugging arrays @*/ #ifndef SLOWLARIS PROTOTYPE void bcopy(const char *, char *, int); #endif /* define a guard area */ #define PAD_MEM_BYTES 32 /* MAX_ALLOC is the greatest number of mallocs outstanding */ #define MAX_ALLOC 4096 /* PAT_ALLOC and PAT_FREE are memory pool checking values */ #define PAT_ALLOC -87097619 /* clear on allocate to facefeed */ #define PAT_FREE -559038737 /* destroy on release to deadbeef */ /* ******************************************************************* */ /*@@*/ /*@ module specific variable declarations @*/ typedef struct { char used_by[16]; /* id of caller */ char *used_ptrs; /* data address returned to user */ char *used_ptrs2; /* data address of starting block for real */ int used_ln; /* line number in calling source code */ int used_size; /* actual size of bytes in block */ } mem_type; local mem_type pmem[MAX_ALLOC + 1]; /* our storage for this program */ local int used_count = -1; local int error_count = 0; local int used_alloc; local int used_free; /* call sequence ids */ local int sts_enable = FALSE; /* on to dump cute info */ local int dbg_enable = FALSE; /* on to dump debug data */ /*@@*/ /* malloc() is defined in stdlib.h */ MODULE void dump_memtables (void) { /*@ # debugging - dump memory tables to screen @*/ /*@ declare variables @*/ int i, j, k; char *tp; /* the returned value */ int *tp2; /*@@*/ /*@ Spew information on malloc failure @*/ fprintf (stderr, "Internal table dump follows... (hope you are ready!)\n"); fprintf (stderr, "Alloc calls %d, Free calls %d, Highest used %d\n", used_alloc, used_free, used_count); j = 0; k = used_count - 1024; if (k < 0) k = 0; /*@ display last 1024 allocation entries @*/ for (i = k; i < used_count; i++) { if (pmem[i].used_size <= 0) continue; fprintf (stderr, "Slot %d, size %d, by %s at %d ", i, pmem[i].used_size, pmem[i].used_by, pmem[i].used_ln); j += pmem[i].used_size; tp = pmem[i].used_ptrs2; tp2 = (int *) tp; if (pmem[i].used_size < 1024 && (int) strlen (tp) < 80) fprintf (stderr, "%s\n", tp); else fprintf (stderr, "(%x %x %x %x)\n", tp2[0], tp2[1], tp2[2], tp2[3]); } /*@@*/ fprintf (stderr, "Internal total used %d\n", j); /*@@*/ /*@@*/ } MODULE char *mem_alloc (int size, int lineid, char *by_who) { /*@ # Allocate a block of storage (128 byte minimum) input: The minimum size to allocate output: min 128 bytes + 10% @*/ /*@ declare variables @*/ static int i; static int slot; static char *tp; /* the returned value */ static int *clr; /*@@*/ /*@ house keep number of calls @*/ used_alloc++; /* count the calls to allocate */ /*@@*/ /*@ trap bogus allocate calls - convert to 128 byte requests @*/ if (size <= 0) { fprintf (stderr, "Internal null request for memory %s %d %d %d\n", by_who, size, used_alloc, used_free); size = 128; } /*@@*/ /*@ determine a slot to place request into @*/ if (used_count < 0) { /*@ initialize array if in a virgin state @*/ for (i = 0; i < MAX_ALLOC; i++) { pmem[i].used_by[0] = '\0'; /* null out who field */ pmem[i].used_ptrs = NULL; pmem[i].used_ptrs2 = NULL; pmem[i].used_size = 0; pmem[i].used_ln = 0; /* and line number */ } slot = 0; used_count = 0; /* initialize */ /*@@*/ } else { /*@ find an empty slot @*/ slot = -1; for (i = 0; i <= used_count; i++) { if (pmem[i].used_size <= 0) { slot = i; break; } } if (slot < 0) slot = ++used_count; /*@@*/ } /*@@*/ /*@ die if unable to allocate a slot for request @*/ if (slot >= MAX_ALLOC) { fprintf (stderr, "Internal allocation past MAX_ALLOC %s %d %d %d\n", by_who, slot, 0, MAX_ALLOC); dump_memtables (); exit (-1); } /*@@*/ /*@ force byte count to 128 min + 10% and a multiple of 8 @*/ pmem[slot].used_size = size + (size / 10) + PAD_MEM_BYTES + PAD_MEM_BYTES; if (pmem[slot].used_size < 128) pmem[slot].used_size = 128; i = pmem[slot].used_size & 7; if (i != 0) pmem[slot].used_size += (8 - i); /*@@*/ /*@ stash the id provided by the calling system @*/ strncpy (pmem[slot].used_by, by_who, 15); pmem[slot].used_ln = lineid; /*@@*/ /*@ ask the system for the space @*/ tp = malloc (pmem[slot].used_size); pmem[slot].used_ptrs = tp; pmem[slot].used_ptrs2 = tp + PAD_MEM_BYTES; if (tp == NULL) { perror ("Memory allocation failure"); fprintf (stderr, "Internal malloc failed for slot %d size %d by %s sequence %d\n", slot, pmem[slot].used_size, by_who, used_alloc); dump_memtables (); exit (-1); } /*@@*/ /*@ clear the array to a special poison pool value if debugging @*/ if (dbg_enable && sts_enable) { clr = (int *) tp; for (i = 0; i < pmem[slot].used_size / 4; i++) clr[i] = PAT_ALLOC; } /*@@*/ /*@ force first two bytes to null to make dbx happy @*/ tp[PAD_MEM_BYTES] = '\0'; tp[PAD_MEM_BYTES + 1] = '\0'; /*@@*/ /*@ return an offset to this pool address to make under/overflows visible @*/ return (pmem[slot].used_ptrs2); /*@@*/ /*@@*/ } MODULE local int find_mem_slot (void *ptr, char *by_who, int lineid) { /*@ # Find a free or occupied memory slot @*/ /*@ declare variables @*/ static int i; static int slot; static long tpl, tph, tpt; /*@@*/ /*@ initialize variables @*/ slot = -1; /*@@*/ /*@ attempt a fast lookup of address @*/ for (i = 0; i <= used_count; i++) { if (ptr == pmem[i].used_ptrs2) { slot = i; break; } } /*@@*/ /*@ fall back to offset pointer recover if not valid still @*/ if (slot < 0) { tpt = (long) ptr; for (i = 0; i <= used_count; i++) { tpl = (long) pmem[i].used_ptrs; tph = tpl + pmem[i].used_size; if (tpt >= tpl && tpt <= tph) { slot = i; fprintf (stderr, "Internal deallocating offset pointer in slot %d by %s at line %d\n", slot, by_who, lineid); break; } } } /*@@*/ /*@ abort on totally invalid pointer @*/ if (slot < 0) { fprintf (stderr, "Internal handed illegal pointer %x by %s at line %d ", ptr, by_who, lineid); if (ptr != NULL && (int) strlen (ptr) < 80) fprintf (stderr, "%s", ptr); fprintf (stderr, "\n"); } /*@@*/ /*@ return location of data @*/ return (slot); /*@@*/ /*@@*/ } MODULE void mem_free (void *ptr, int lineid, char *by_who) { /*@ # Release a block of memory @*/ /*@ declare local variables @*/ static int i; static int slot; static int *clr; /*@@*/ /*@ house keep call counts @*/ used_free++; /* account for the release */ /*@@*/ /*@ trap call before initialize @*/ if (used_count < 0) { fprintf (stderr, "Internal releasing before allocating %x by %s\n", ptr, by_who); ptr = NULL; return; } /*@@*/ /*@ map address to slot and abort if invalid @*/ slot = find_mem_slot (ptr, by_who, lineid); if (slot < 0) { ptr = NULL; return; } /*@@*/ /*@ if debugging then verify underrun and overrun status then clear data @*/ if (dbg_enable && sts_enable) { clr = (int *) pmem[slot].used_ptrs; for (i = 0; i < PAD_MEM_BYTES / 4; i++) { /*@ check and report underflow errors @*/ if (clr[i] != PAT_ALLOC) { fprintf (stderr, "Internal array corruption low pointer %x by %s at %d from %s at %d\n", ptr, by_who, lineid, pmem[slot].used_by, pmem[slot].used_ln); fprintf (stderr, "i = %d clr[i] = %x\n",i, clr[i]); break; } /*@@*/ } for (i = (pmem[slot].used_size - PAD_MEM_BYTES) / 4; i < pmem[slot].used_size / 4; i++) { /*@ check and report overflow errors @*/ if (clr[i] != PAT_ALLOC) { fprintf (stderr, "Internal array corruption high pointer %x by %s at %d from %s at %d\n", ptr, by_who, lineid, pmem[slot].used_by, pmem[slot].used_ln); fprintf (stderr, "i = %d clr[i] = %x\n",i, clr[i]); break; } /*@@*/ } /*@ erase pool of memory @*/ for (i = 0; i < pmem[slot].used_size / 4; i++) clr[i] = PAT_FREE; /*@@*/ } /*@@*/ /*@ release storage and house keep the counters @*/ free (pmem[slot].used_ptrs); ptr = NULL; pmem[slot].used_ptrs = NULL; pmem[slot].used_size = 0; while (pmem[used_count].used_ptrs == NULL && used_count > 0) used_count--; /*@@*/ /*@@*/ } MODULE char *mem_realloc (void *ptr, int size, int lineid, char *by_who) { /*@ # expand or contract a given block of memory @*/ /*@ declare variables @*/ int slot; char *new_ptr; /* memory pointer to return */ /*@@*/ /*@ null argument defaults to a staight mem_alloc @*/ if (ptr == NULL) { return (MEM_ALLOC (size)); } /*@@*/ /*@ check and handle call before initialize @*/ if (used_count < 0) { fprintf (stderr, "Internal realloc before allocating %x at %d by %s\n", ptr, lineid, by_who); return (MEM_ALLOC (size)); } /*@@*/ /*@ find current slot and abort on bad data @*/ slot = find_mem_slot (ptr, by_who, lineid); if (slot < 0) { return (MEM_ALLOC (size)); /* bad boy pointers are ignored */ } /*@@*/ /*@ ignore shrinkage of space requests @*/ if (size <= pmem[slot].used_size) { return (ptr); /* no change */ } /*@@*/ /*@ allocate new storage and copy, then release old data @*/ new_ptr = MEM_ALLOC (size); #ifndef SLOWLARIS bcopy (ptr, new_ptr, pmem[slot].used_size); #else memcpy (new_ptr, ptr, pmem[slot].used_size); /* sun has to be different */ #endif MEM_FREE (ptr); return (new_ptr); /*@@*/ /*@@*/ } From jxh@ibm12.biosym.com Thu Mar 16 16:13:18 1995 Received: from bioc1.biosym.com for jxh@ibm12.biosym.com by www.ccl.net (8.6.10/930601.1506) id PAA29123; Thu, 16 Mar 1995 15:51:30 -0500 Received: from ibm12.biosym.com by bioc1.biosym.com (5.64/0.0) id AA24749; Thu, 16 Mar 95 12:51:50 -0800 Received: by ibm12.biosym.com (AIX 3.2/UCB 5.64/4.03) id AA19339; Thu, 16 Mar 1995 12:51:49 -0800 Date: Thu, 16 Mar 1995 12:51:49 -0800 From: jxh@biosym.com (Joerg Hill) Message-Id: <9503162051.AA19339@ibm12.biosym.com> To: CHEMISTRY@ccl.net Subject: Re: CCL: BSSE Sorry for wasting bandwidth, but some mailers seem to be unable to process mails in ISO-8859-1 correctly. So here it is again: Peter Winn asks: > What is the current consensus on the affect of > basis set superposition errors on ab initio quantum > calculations???? In particular I would be interested > in:- > > (i) The affect it has on interatomic distances when > optimising a group of molecules. > > (ii) The overall expected error in interaction > energies one might expect from a group of optimised > molecules. > > (iii) Identifying you have a BSSE > > (iv) Correcting for BSSE. > > (v) A reference covering the above problems in a consistent manner. > > I have found many references that deal with BSSE > but nothing that really gives an overview of the > whole problem. The BSSE is always present if you are doing calculations on intermolecular interactions. In this case you will do a calculation on your molecules alone (monomers) and then you will put these molecules together (complex, supermo- lecule approach) and do another calculation. From the results of all these calculations you will try to figure out what happens when the molecules interact. Unfortunately, by putting all molecules together, you add additional basis functions to your monomers (the basis functions of the other monomers), so that your basis set becomes more flexible (and the energy therefore lower) compared to your monomer calculations. Or, to put it another way, the electrons in your monomer are described by basis functions of the other monomers. There- fore, your BSSE depends on the quality (size) of your basis set. If you use a larger basis set, your electrons will be described more complete in the monomer basis, thus reducing the BSSE. Since the BSSE affects the energy it will affect all properties calculated: interaction energies, the geometry changes going from monomers to the complex etc. The standard method of correcting for the BSSE is the counterpoise correction method of Boys and Bernardi (S.F. Boys, F. Bernardi; Mol. Phys. 19, 553 (1970)). This method requires additional calculations to be performed for the monomers: You take the basis functions as they are in the complex, but remove all the atoms which do not belong to your monomer (creating so-called ghost functions). Then you do a calculation for your monomer with this larger basis set. Your BSSE for the interaction energy is then: BSSE = (E(a)-E(a*)) + (E(b)-E(b*)) (1) where E(a) and E(b) are the energies of the monomers without ghost functions and E(a*) and E(b*) are the energies of the monomers with ghost functions. (Note: This procedure in ambigious if you have more than two molecules; L. Turi, J. J. Dannenberg; J. Phys. Chem. 97, 2488 (1993).) The number you get from Eq. (1) tells you something about the quality of your basis set. It should be significantly smaller than the effect you are looking at (can be hard to achieve). If you are using a correlated method you will see a much larger BSSE with the same basis set compared to SCF. This has to do with having additional virtual orbitals in the complex (S. Saebx, W. Tong, P. Pulay; J. Chem. Phys., 98, 2170 (1993)). As mentioned above, the BSSE also affects the geometry. I haven't seen any paper which has done a BSSE correction for geometries. In principle you have to do the same correction at each step of your geometry optimization calculating the gradient from the corrected energy. The counterpoise correction also does not recover all of the BSSE, since it does not allow the ghost functions to change their positions in space. There are a lot of references for the BSSE (from a previous discussion of this topic on the CCL, you may look in the CCL archives for more): - "Gaussian Basis sets for Molecular Calculations", S. Huzinaga, Elsevier (1991) - "Ab Initio Calculations", P. Carsky and M. Urban, Springer- Verlag, Lecture Notes in Chemistry, 1980. - "Intermolecular Complexes", P. Hobza and R. Zahradnik, Academia, Prague (1988) Joerg-R. Hill -------------------------------------------------------------------------------- Dr. Joerg-Ruediger Hill | Every attempt to employ mathematical methods in the Biosym Technologies, Inc. | study of chemical questions must be considered pro- 9685 Scranton Road | foundly irrational and contrary to the spirit of San Diego, CA 92121-2777 | chemistry ... If mathematical analysis should ever USA | hold a prominent place in chemistry - an aberration | which is happily almost impossible - it would Phone (619) 546-5508 | occasion a rapid and widespread degeneration of Fax (619) 458-0136 | that science. E-mail jxh@biosym.com | A. Comte, 1830 -------------------------------------------------------------------------------- The opinions expressed in this message are my personal opinions and no offical statements of Biosym Technologies, Inc. For informations about Biosym products send mail to: rcenter@biosym.com. -------------------------------------------------------------------------------- From garrett@scripps.edu Thu Mar 16 19:13:00 1995 Received: from scripps.edu for garrett@scripps.edu by www.ccl.net (8.6.10/930601.1506) id TAA02649; Thu, 16 Mar 1995 19:01:59 -0500 Received: from jonah.scripps.edu by scripps.edu (5.61/1.34) id AA26552; Thu, 16 Mar 95 16:01:55 -0800 Received: from eve.Scripps.EDU by jonah.Scripps.EDU (4.1/SMI-4.1/TSRI1.0) id AA23011; Thu, 16 Mar 95 16:00:18 PST Received: by eve.Scripps.EDU (5.0/SMI-SVR4) id AA05070; Thu, 16 Mar 1995 16:00:19 +0800 Date: Thu, 16 Mar 1995 16:00:19 +0800 From: garrett@scripps.edu (Garrett M. Morris) Message-Id: <9503170000.AA05070@eve.Scripps.EDU> To: chemistry@ccl.net Subject: Re: CCL:malloc etc. on DEC Alpha Cc: garrett@scripps.edu X-Sun-Charset: US-ASCII Content-Length: 2177 -> Date: Tue, 14 Mar 95 10:36:19 +0530 -> From: Mrigank -> Subject: CCL:malloc etc. on DEC Alpha -> -> HI -> -> I am finding in using 'malloc' family or routines[malloc, free etc.] on our DEC -> alpha machines running OSF/1. whenever they are called the program gives -> segmentaion fault or memory fault and aborts. The code works very fine on other -> machines. These are veru eesential in many huge comp. chem programs where -> memory need to allocated as needed rather than fixed arrays and i can not -> change the developed code for it is pain as well as not usefull. -> not have food, they call me communist - Archbishop Camaran -> Apparently, Mrigank, On DEC machines, you *must* supply a 64-bit (i.e. "long" or "size_t") argument to malloc. If you do not, you can expect spectacular core dumps. I checked the "typedef" for size_t on a variety of architectures, in the file "/usr/include/stdlib.h", and found this: Architecture/OS "typedef ... size_t;" --------------- --------------------------------------- sun4/SunOS4 int sun4/sunOS5.3 unsigned int sgi4D/IRIX4.0.5 unsigned sgi4D/IRIX5.2 unsigned int } if _MIPS_SZLONG == 32 hppa/HP-UXA.09.01 unsigned int convex/ConvexOS10.1.184 unsigned int BUT... sgi4D/IRIX5.2 unsigned long } if _MIPS_SZLONG == 64 alpha/OSF1V3.0 unsigned long I would recommend explicitly casting your malloc-argument correspondingly. I hope this helps! Garrett ----------------------------------------- ------------------------------------ | Garrett M. Morris, D.Phil., Research Associate, _________ | | | | _____ | | Department of Molecular Biology, MB-5, | garrett@scripps.edu | | _ | | The Scripps Research Institute, | | | | | | 10666 North Torrey Pines Road, | Tel: + (619) 554-4392 | | | | La Jolla, CA 92037, U.S.A. | Fax: + (619) 554-6860 | | | | | ----------------------------------------- ------------------------------------ From 5GK9SUNJ@VMS.CSD.MU.EDU Thu Mar 16 21:13:02 1995 Received: from VMSA.CSD.MU.EDU for 5GK9SUNJ@VMS.CSD.MU.EDU by www.ccl.net (8.6.10/930601.1506) id UAA03936; Thu, 16 Mar 1995 20:39:53 -0500 Received: from VMS.CSD.MU.EDU by VMS.CSD.MU.EDU (PMDF V4.3-10 #8872) id <01HO7RGDRRAO939N5W@VMS.CSD.MU.EDU>; Thu, 16 Mar 1995 19:39:50 -0600 (CST) Date: Thu, 16 Mar 1995 19:39:50 -0600 (CST) From: "JIANGUO SUN, CHEMISTRY DEPT., MARQUETTE U." <5GK9SUNJ@VMS.CSD.MU.EDU> Subject: Summary of chemistry WWW sites To: chemistry@ccl.net Message-id: <01HO7RGDSALE939N5W@VMS.CSD.MU.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: 5GK9SUNJ MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters: To reponse the requests from many people who are also interested in Chemistry WWW sites, I summarized the replies here. Thanks for all your helps. Jianguo ************************************************************************** My original question was: > Could anyone tell me where I can find some WWW webs about chemistry >resources? I need some samples (any chemistry) to build ours. The replies are: #1 **************************** From: IN%"jkl@ccl.net" "Jan Labanowski" 13-MAR-1995 22:27:50.91 Did you try: http://www.ccl.net/chemistry.html and clicked on hypertext in "Other Sites of Interest?" Then you can usually download the pages and save them as files, and see what other people do. Jan jkl@ccl.net #2 *************************** From: IN%"thys@uia.ua.ac.be" "Gerd Thys" 14-MAR-1995 00:37:40.88 Feel free to have a look at my WWW-page... I have collected more than 100 links to chemistry-related resources. You can access my Chemistry-page through http://www.uia.ac.be/u/thys/chem.html or if you want, you can also look at my root-page, which includes other (=non-chemistry) interesting stuff: http://www.uia.ac.be/u/thys/index.html hope this is of any help best regards Gerd ---------------------------------------------------------------------------- Gerd Thys Ph.D. Student Structural Chemistry Group University of Antwerp (UIA) Universiteitsplein 1 E-mail: thys@uia.ua.ac.be B-2610 wilrijk URL: http://www.uia.ac.be/u/thys/index.html BELGIUM ---------------------------------------------------------------------------- #3 ************************************ From: IN%"nielsl@sci.kun.nl" "Niels van der Laag" 14-MAR-1995 01:56:44.96 Hi there, I'm a student at the university of Nijmegen, The Netherlands. The students here have there WWW-pages. Unfortunaly the depart- ment not yet. The address is: http://www.sci.kun.nl/sigma/ Succes Niels van der Laag student computational chemistry #4 ************************************ From: IN%"noy@tci002.uibk.ac.at" 14-MAR-1995 02:57:20.92 Hi!, An very complete, but not exhaustive index lists are of chemistry homepage is at http://www.chem.ucla.edu/chempointers.html take care. Noy ---------------------------------------------------------------------------- E-mail: noy@tci2.uibk.ac.at (University of Innsbruck) noy@atc.atccu.chula.ac.th (Bangkok) (Permanent E-mail address) Homepage http://www-c724.uibk.ac.at/noy/ http://atc.atccu.chula.ac.th/noyhome/ ----------------------------------------------------------------------------- *** Love is easy to start but hard to stop #5 ******************************************** From: IN%"ostertag@alf.biochem.mpg.de" "Georg Ostertag" 14-MAR-1995 03:49:04.11 I send you the adresses of 4 chemistry - www servers in germany which are my preferred: http://www.chemie.fu-berlin.de/index.html Freie Universitaet Berlin CHEMnet WWW Entry Point ==> outfit very interesting! http://www.pc.chemie.th-darmstadt.de/ Physical Chemistry, Technische Hochschule Darmstadt http://derioc1.organik.uni-erlangen.de/ccc-welcome.html CCC (Computer Chemistry Club) Erlangen HOMEPAGE http://pctc.chemie.uni-erlangen.de/fakultaet/chemie.html Erlangen - Chemie Hope this helps. Georg. #6 ************************************** From: IN%"webmastr@organik.uni-erlangen.de" "CCC Webmaster" 14-MAR-1995 06:01:35.78 You are invited to have a look at the WWW pages of the CCC (Computer Chemistry Center) in Erlangen URL = http://www.organik.uni-erlangen.de/ Good webbing A.Dransfeld as ( webmastr@ccc.uni-erlangen.de ) #7 *************************************** From: IN%"rs0thp@rohmhaas.com" 14-MAR-1995 06:59:32.20 Chemistry Home Page

Chemistry Home Page

Some sites

  • Phoenix Polymers, Inc., a compounder of proprietary engineering thermoplastics
  • Lists of Internet Chemistry Resources at

    Anonymous FTP Servers

    -- Sincerely, Thomas Pierce - THPierce@RohmHaas.Com - Computational Chemist "These opinions are those of the writer and not the Rohm and Haas Company." #8 ****************************************************** From: IN%"rosas@irisdav.chem.vt.edu" "Victor M. Rosas Garcia" 14-MAR-1995 07:40:29.09 You can get started with these sites: Ohio Supercomputer Center

    WWW Chem Servers

    Chemistry Page (EINET)

    Cambridge Crystallographic Data Center

    The Geometry Center

    Magnetic Resonance Home Page

    WSU Computer Animations

    Hope this helps. Victor. #9 ***************************************** From: IN%"nauss@ucmod2.che.uc.EDU" 14-MAR-1995 08:07:05.73 You can try our site (which has not been officially opened to the public) at http://ucmodl.che.uc.edu/ucchem.html. Also, many people find the UCLA site useful (http://www.chem.ucla.edu/chempointers.html). Personally, I find it too cluttered. Two other places you may like are: Duke - http://www.chem.duke.edu/ SUNY-Binghamton - http://chemiris.chem.binghamton.edu:8080/ Good luck. Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC http://ucmodl.che.uc.edu/~nauss/homepage.html * **************************************************************************** #10 ******************************************** From: IN%"LSTEFFEN@fair1.fairfield.edu" 14-MAR-1995 09:13:06.03 Here two good sites to get you started: http://akebono.stanford.edu/yahoo/Science/Chemistry/ http://www.chem.ucla.edu/chempointers.html and a couple of my all time favorites: http://www.nih.gov/molecular_modeling/gateway.html http://www.ch.ic.ac.uk/GIC/ Hope this helps get you started, L. Kraig Steffen Assistant Professor of Chemistry Fairfield University, Fairfield CT 06430 203 254-4000 ext 2254 lsteffen@fair1.fairfield.edu lsteffen@aol.com #11 *********************************************** From: IN%"ezequiel@wucmd.wustl.edu" "Ezequiel Q. Morales" 14-MAR-1995 11:22:38.17 Hi, I have several addresses that can be interesting for you: Scientific Web Resources http://boris.qub.ac.uk/edward/index.html Science:Chemistry http://akebono.stanford.edu/yahoo/Science/Chemistry Organic Chemistry Resources http://www.chem.vt.edu/chem-ed/org-home.html NMR Information Server http://micro.ifas.ufl.edu Chemist's Art Gallery http://www.csc.fi/lul/chem/graphics.html Enjoy them ------------------------------------------------------------------------------- Ezequiel Quintana Morales Washington University, School of Medicine Dept. of Molecular Biology and Pharmacology Campus Box 8103, 660 S. Euclid Ave. St. Louis, MO 63110 Tel: + 1 314 362 29 87 Fax: + 1 314 362 70 58 e-Mail: ezequiel@wucmd.wustl.edu ------------------------------------------------------------------------------- #12 ****************************************** From: IN%"Jeffrey.Gosper@brunel.ac.uk" 14-MAR-1995 11:25:09.49 Try http://akebono.stanford.edu/yahoo/Science/Chemistry/ and http://wwwhost.cc.utexas.edu/world/instruction/index.html and http://www.ch.ic.ac.uk/local/organic/ if you produce a list please let me know. > ######################################################### # Dr. Jeff Gosper # # Dept. of Chemistry # # BRUNEL University # # Uxbridge Middx UB8 3PH # # voice: 0895 274000 x2187 # # facsim: 0895 256844 # # internet/email/work: Jeffrey.Gosper@brunel.ac.uk # # internet/WWW: http://http2.brunel.ac.uk:8080/~castjjg # ######################################################### #13 ******************************************************** From: IN%"bear@ellington.pharm.arizona.edu" 14-MAR-1995 12:49:36.44 you may look at my page of net link tools http://copsg2.pharm.arizona.edu/~bear please leave an email there to let me know what you think bear ___ __ ___ _____ ___ _____ ___ (___ l .) /\ \ / \ \#\ \ / \ \/\ \ / ___)OARING |__)EAR /\ \ / \ \#\ \ / \ \ \ \ Cyber-Chemist, Molecular Design \__\/ \__\#\_.\/ \__\ \__\/ bear@ellington.pharm.arizona.edu N+ O-Tyr-topo UA New Pharmacy 404 Tucson 85721 Topoisomerase reference URL: http://copsg2.pharm.arizona.edu/~bear/top/top * / \|/ Listening may be the most important thing we do today! (=) #14 ******************************************** From: IN%"D.Winkler@chem.csiro.au" 14-MAR-1995 18:35:03.99 Try http://www.rpi.edu/dept/chem/cheminfo/chemres.html Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 CSIRO: http://www.csiro.au Clayton, Australia. #15 **************************************** From: IN%"zhy@pchsgi25.IPC.PKU.EDU.CN" 14-MAR-1995 18:48:33.95 I know a place in stanford which provides rich informations on chemistry http://akebono.stanford.edu/yahoo/Science/Chemistry/ ---------------------------------------------------------------------- Henry Hongyu Zhang | zhy@pchsgi25.ipc.pku.edu.cn Molecular Design Laboratory | Tel: 861-2501490 Institute of Physical Chemistry | Fax: 861-2501725 Peking University | Peking 100871 , China | #16 ********************************************** From: IN%"pateta@vents.uji.es" 15-MAR-1995 00:37:51.40 you can find in: http://akebono.stanford.edu/yahoo/ an interactive index about any field. About chemistry, one good site to jump to another is : http://www2.shef.ac.uk/chemistry/chemistry-home.html Have a nice trip ... Augusto Cesar ----------------------------------------+--------------------------------------- | Augusto Cesar de Camargo Neto - Pateta | Keith Nelson: You can't judge a Universitat Jaume I | ------------- book by its cover ... Departament de Ciencies Experimentales | Grupo de Quimica Quantica | Watts: Yeah, but you can tell how Apartat 224 | ----- much it's gonna cost. 12008 - Castello | Spain | in Some Kind of Wonderfull (1987) |--------------------------------------- Phone: +34 64 34-5700 ext. 2309 | Fax: +34 64 34-5654 | John Keating: Carpe diem !!! | ------------ e-mail: pateta@migjorn.uji.es | | in Dead Poets Society (1989) ----------------------------------------+--------------------------------------- #17 ******************************************** From: IN%"wtwinter@mailbox.syr.edu" "William T. Winter" 15-MAR-1995 01:40:32.88 http://glucose.esf.edu which I have not announced publicly but which does have lots of pointers. you are welcome to look warning, since I am still doing a lot of tinkering, this site shuts down without warning aperiodically =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786 #18 ***************************************** From: IN%"arthur@pchindigo2.IPC.PKU.EDU.CN" "Wang Arthur" 15-MAR-1995 02:09:13.85 You will find the following address helpful: http://www.rpi.edu/dept/chem/cheminfo/chemres.html Good luck. Arthur +-----------------------------------------------------------+ | | | Arthur Wang Doctoral Candidate | | | | Molecular Design Lab | | Institute of Physical Chemistry, Peking University | | Beijing 100871, P.R.China | | | | E-mail: arthur@pchindigo2.ipc.pku.edu.cn | | Telephone: 86-1-2501490 | | WWW: ftp://162.105.177.1/sys/www/arthur/homepage.html | | http://www.ipc.pku.edu.cn/arthur/homepage.html | | | +-----------------------------------------------------------+ #19 ***************************************** From: IN%"szilagyi@indy.mars.vein.hu" "Robert K. Szilagyi" 16-MAR-1995 01:25:36.52 Try our server! We have some excellent links to chemistry related documents! Good luck, Rob ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Robert K. Szilagyi University of Veszprem METMOD FF research fellow Dept. Org. Chem. L1 Email: szilagyi@miat0.vein.hu Veszprem, H-8201 L2 | R1 szilagyi@indy.mars.vein.hu Egyetem u. 10 >W=C< Phone: +36-(88)-422022/137 P.O.Box 158 L3 | R2 FAX: +36-(88)-426016 HUNGARY L4 http://indy.mars.vein.hu:8000/molmod.html ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~