From ferenc@rchsg8.chemie.uni-regensburg.de Fri Jul 1 03:04:37 1994 Received: from comsun.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.9/930601.1506) id DAA03057; Fri, 1 Jul 1994 03:02:05 -0400 Received: from rchsg8.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA17926 (5.65c/IDA-1.4.4 for ); Fri, 1 Jul 1994 09:02:02 +0200 Received: by rchsg8.chemie.uni-regensburg.de (931110.SGI/URRZ-Sub-1.5-irix) (for CHEMISTRY@ccl.net) id AA29110; Fri, 1 Jul 94 09:00:03 +0200 Date: Fri, 1 Jul 94 09:00:03 +0200 From: Ferenc.Molnar@chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9407010700.AA29110@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: accesible volume Dear Netters: A friend of mine asked me to submit the following request to the CCL. Please direct your replies to him. >My name is Johannes Richardi and I make my PHD at the institut for physical >chemistry of Prof. Barthel in Regensburg. >I am looking for programs I can use to calculate the approximate volume of a >molecule accessible to molecules of the same kind. >I would like to use this program for example to approximate the accessible >volume of Dimethylacetamide (DMA). >I have calculated the bond angles and lengths of DMA and I know the >radii of the atoms of DMA by computer simulation. >Please send me information under johannes.richardi@chemie.uni-regensburg.de > Thank you very much in advance. > Johannes Best regards, Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): Ferenc.Molnar@chemie.uni-regensburg.de --------------------------------------------------------------------------- :-) I wish to have no connection with any ship that does not sail fast, for I intend to go in harm's way. -- John Paul Jones, USN 1747-1792 ;-) --------------------------------------------------------------------------- From nieuwpoort@chem.rug.nl Fri Jul 1 09:04:43 1994 Received: from rugch4.chem.rug.nl for nieuwpoort@chem.rug.nl by www.ccl.net (8.6.9/930601.1506) id IAA06929; Fri, 1 Jul 1994 08:27:23 -0400 Message-Id: <199407011227.IAA06929@www.ccl.net> Received: from rugch5.chem.rug.nl by rugch4.chem.rug.nl with SMTP (1.37.109.4/16.2) id AA23935; Fri, 1 Jul 94 14:27:22 +0200 Received: from theochem6.chem.rug.nl by rugch5.chem.rug.nl with SMTP (1.37.109.4/16.2) id AA03512; Fri, 1 Jul 94 14:30:16 +0200 X-Sender: willem@rugch5.chem.rug.nl Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 1 Jul 1994 14:30:35 +0000 To: Kui Zhang From: nieuwpoort@chem.rug.nl (W.C.Nieuwpoort) Subject: Re: CCL:Ques on calculations of La's and Ac's elements Cc: chemistry@ccl.net >Does anyone know of methods which are able to treat Lanthanide and >Actinide elements. I want to calculate a bunch of molecules containing >these elements using either ab initio or semiempirical method. Any >information and suggestion would greatly appreciate. > >Kui Zhang >e-mail: kzhang@miamiu.acs.muohio.edu Hi, An all-electron fully relativistic ab initio calculation on EuO6 has been reported by O. Visser et al in J. Chem. Phys.96 (1992) 2910. For possible other ab initio work you might contact Bert de Jong . Wim Nieuwpoort. W.C. Nieuwpoort Laboratory of Chemical Physics and Materials Science Centre University of Groningen Nijenborgh 4 9747 AG Groningen, The Netherlands ph.+31 50 634372, 634440 (secr), 634441 (fax) e-mail nieuwpoort@chem.rug.nl From aiba@volta.vmsmail.ethz.ch Fri Jul 1 09:13:40 1994 Received: from bernina.ethz.ch for aiba@volta.vmsmail.ethz.ch by www.ccl.net (8.6.9/930601.1506) id IAA07261; Fri, 1 Jul 1994 08:47:06 -0400 Message-Id: <199407011247.IAA07261@www.ccl.net> Received: from VOLTA.vmsmail.ethz.ch by bernina.ethz.ch id <08701-0@bernina.ethz.ch>; Fri, 1 Jul 1994 14:46:48 +0200 X-Vms-To: ethz::"chemistry@ccl.net" To: chemistry@ccl.net From: aiba@volta.vmsmail.ethz.ch (Aiaz Bakassov, Phys. Chem., ETH Zurich) Subject: G92. Two forthcoming summaries Date: Fri, 1 Jul 1994 14:46:48 +0200 Dear netters, I have recently posted two questions (in chronological order): 1. About extraction of core energies and, possibly, of two-electron repulsion integrals from G92; 2. About batch queue control when mixing G92 with some "my_code" both under VMS and under UNIX. First question attracted replies from only one person - Alberto Gobbi, and his advice about core energies worked perfectly. Many many thanks to him. I am checking his other advices. That'll be finished in a day or two. And the summary about question 1 will be posted. Second question attracted a lot of replies, showing thus far that the question is of real interest. Thanks so much ! The spectrum of advices is really very wide. It's a tough task to check them all, but I'll try -- give me a week please for that. Summary will be posted. Sincerely, -------------------------------------------------------- -------------- Aiaz BAKASSOV (English: Ayaz BAKASOV) | Phone: +41 1 632 79 18 Laboratorium fuer Phys. Chemie | FAX: +41 1 632 10 21 ETH-Zuerich (Zentrum) | E-mail: aiba@debye.vmsmail.ethz.ch CH-8092 Zurich, Switzerland | aiba@ir.lpc.ethz.ch -------------------------------------------------------- -------------- From EWING@jcvaxa.jcu.edu Fri Jul 1 10:05:59 1994 Received: from jcvaxa for EWING@jcvaxa.jcu.edu by www.ccl.net (8.6.9/930601.1506) id JAA07719; Fri, 1 Jul 1994 09:13:15 -0400 Received: from jcvaxa.jcu.edu by jcvaxa.jcu.edu (PMDF V4.3-7 #6158) id <01HE6Q6CUHSW8WWKL3@jcvaxa.jcu.edu>; Fri, 1 Jul 1994 09:14:57 EST Date: Fri, 01 Jul 1994 09:14:57 -0500 (EST) From: "DAVID W. EWING (216) 397-4742" Subject: Graduate programs in pharmacognostics? To: chemistry@ccl.net Message-id: <01HE6Q6CX69E8WWKL3@jcvaxa.jcu.edu> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: EWING MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Since many of you on this list are in the medicinal sciences, perhaps you could help me. One of my students is looking for a graduate program in pharmacognostics (pharmacognosy). Which schools have such a program? Thank you for any suggestions you might have. Dave Ewing John Carroll University ewing@jcvaxa.jcu.edu From shenkin@still3.chem.columbia.edu Fri Jul 1 11:04:43 1994 Received: from still3.chem.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.9/930601.1506) id LAA09903; Fri, 1 Jul 1994 11:01:30 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA16944; Fri, 1 Jul 94 11:01:04 -0400 From: "Peter Shenkin" Message-Id: <9407011100.ZM16942@still3.chem.columbia.edu> Date: Fri, 1 Jul 1994 11:00:53 -0400 In-Reply-To: "DAVID W. EWING (216) 397-4742" "CCL:Graduate programs in pharmacognostics?" (Jul 1, 9:14am) References: <01HE6Q6CX69E8WWKL3@jcvaxa.jcu.edu> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "DAVID W. EWING (216) 397-4742" , chemistry@ccl.net Subject: Re: CCL:Graduate programs in pharmacognostics? Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Jul 1, 9:14am, DAVID W. EWING (216) 397-4742 wrote: > Subject: CCL:Graduate programs in pharmacognostics? > Since many of you on this list are in the medicinal sciences, perhaps you > could help me. One of my students is looking for a graduate program in > pharmacognostics (pharmacognosy). Which schools have such a program? I'd advise him to be very careful. This is only one step away from pharmatheism, and we all know where that leads. :-) More seriously, what the hell is (or are) pharmacognostics? I ask publically, rather than privately, because I suspect that other inquiring minds might also want to know.... -P. -- ******* After the revolution, everyone will have a home page... ****** *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* *New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * *** ... but the Internet will be too busy for anyone to access it. *** From vijay@rose.chem.wesleyan.edu Fri Jul 1 12:04:48 1994 Received: from rose.chem.wesleyan.edu for vijay@rose.chem.wesleyan.edu by www.ccl.net (8.6.9/930601.1506) id LAA10321; Fri, 1 Jul 1994 11:26:11 -0400 Received: from jellyfish.chem.wesleyan.edu by rose.chem.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA20763; Fri, 1 Jul 1994 11:24:17 -0400 Date: Fri, 1 Jul 1994 11:24:17 -0400 Message-Id: <9407011524.AA20763@rose.chem.wesleyan.edu> X-Sender: vijay@rose Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: vijay@rose.chem.wesleyan.edu (S. Vijayakumar) Subject: RMSD X-Mailer: mikes@bioch.ox.ac.uk wrote: : I am looking for a software package which will enable me to : least-squares-fit and find the rmsds between two structures. The : complicating factor is that I want to do it on structures of different : amino acid sequences, to fit on the backbone and all relevent atoms, and : give an rmsd based on this. : : I have tried XPLOR but it seems to insist the molecules are : identical. I would also like to have the backbone rmsd printed out on a : residue-by-residue basis. : ----Other stuff deleted---------------- and brian@bert.chem.wsu.edu responded, > I've run into the same problem with the proteins > I work with. Since you seem to be primarily interested in > the backbone RMSD (as I was), then why don't you edit out > all the side chains (i.e. make all the side chains =GLY). The origin of the problem is as follows: Two proteins of length 'n' and 'm' can be superposed in n-m+1 ways, assuming connectivity is retained and the superposition is unidirectional, i.e. N-terminal end to C-terminal end. The majority of the programs circumvent this problem by requiring that the molecules be identical or contain the same number of atoms! Thus if you can specify the residues ranges for each protein and apply a suitable selection criteria such that there is a one-to-one correspondence between the two sets of atoms (this necessitates equal number of atoms), then most commercial programs can superpose the two structures. I am, however, not aware if they can spit out residue based RMS. If you can write a script to extract only the necessary coords., I have a home grown program that can superpose any two structures and spit out residue based RMS. Unfortunately it does not read a variety of input formats as is, but you can modify the code to read in your coords. with minimal effort. If you send me e-mail I can mail you the code. Hope this helps. Best wishes, Vijay S. Vijayakumar Department of Chemistry Wesleyan University Middletown, CT 06459 E-mail: vijay@rose.chem.wesleyan.edu Voice: (203) 347-9411, x3196 Fax: (203) 344-7960 From KEWISE@aardvark.ucs.uoknor.edu Fri Jul 1 12:09:10 1994 Received: from aardvark.ucs.uoknor.edu for KEWISE@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.9/930601.1506) id LAA10126; Fri, 1 Jul 1994 11:10:10 -0400 From: Message-Id: <199407011510.LAA10126@www.ccl.net> Date: Fri, 1 Jul 94 10:10 CDT Subject: Summary of Responses to Mopac 6.0 Makefile Question To: CHEMISTRY@ccl.net X-VMS-To: IN%"CHEMISTRY@ccl.net" Netter's The following is an abridged summary of the replies that I recieved in response to my query about Mopac 6.0 Makefiles. Everyone's help was greatly appreciated and I hope these postings will be of as much use to others as they were to me. I've included a copy of the appropriate Makefile as well as an alternative method of installation suggested by Peter Bladon. Attached at the end is a message that I recieved from Robert Fraczkiewicz about an error that he encountered while installing the ESP code that seems to be related to the type of arrays used in the program. I cannot answer his question in this regard, possibily someone else will be able to. In response to his question about the parameterization of Mopac (or MNDO,AM1,etc) for transition metals, my understanding is that it is a lack of sufficient experimental data for compounds containing these elements that has hindered the development of reliable parameters. However, the most recent commercial version of AMPAC (2.0 or 3.0?) claims to have parameters for iron. I suspect that these will be used rather cautiously until their accuracy has been proven. (If interested you might try contacting Andy Holder, but I don't have his e-mail address) In response to the queries about where to find the public domain version of Mopac 6.0, try the anonymous ftp site at the Ohio Supercomputer Center. www.ccl.net in the directory: /pub/chemistry/software/SOURCES/FORTRAN/mopac6_sources I'm sure that it is available at other sites and perhaps someone else will post these for the list. Let me finish by apologizing for taking so long to post this summary, but I wanted to make sure that all the responses were in. Thanks again to all who helped out. Kris Wise University of Oklahoma Department of Chemistry and Biochemistry KEWISE@aardvark.ucs.uoknor.edu ******************************************************************************** ******************************************************************************** ******************************************************************************** ******************************************************************************** MOPAC 6.0 makefile: --------------------------- Cut Here -------------------------------- flAGS = FFLAGS = -O2 -g3 -static DEST = . LDFLAGS = LIBS = LINKER = f77 LINTFLAGS = MAKEFILE = Makefile PRINT = pr PROGRAM = mopacrsm.exe EXTHDRS = HDRS = OBJS = aababc.o \ analyt.o \ anavib.o \ axis.o \ block.o \ bonds.o \ brlzon.o \ calpar.o \ capcor.o \ cdiag.o \ chrge.o \ cnvg.o \ compfg.o \ datin.o \ dcart.o \ delmol.o \ delri.o \ denrot.o \ densit.o \ depvar.o \ deri0.o \ deri1.o \ deri2.o \ deri21.o \ deri22.o \ deri23.o \ deritr.o \ deriv.o \ dernvo.o \ ders.o \ dfock2.o \ dfpsav.o \ diag.o \ diat.o \ diat2.o \ diis.o \ dijkl1.o \ dijkl2.o \ dipind.o \ dipole.o \ dofs.o \ dot.o \ drc.o \ drcout.o \ ef.o \ enpart.o \ exchng.o \ ffhpol.o \ flepo.o \ fmat.o \ fock1.o \ fock2.o \ force.o \ formxy.o \ forsav.o \ frame.o \ freqcy.o \ geout.o \ geoutg.o \ getgeg.o \ getgeo.o \ getsym.o \ gettxt.o \ gmetry.o \ gover.o \ grid.o \ h1elec.o \ haddon.o \ hcore.o \ helect.o \ hqrii.o \ ijkl.o \ interp.o \ iter.o \ jcarin.o \ linmin.o \ local.o \ locmin.o \ mamult.o \ matout.o \ matpak.o \ meci.o \ mecid.o \ mecih.o \ mecip.o \ mndo.o \ moldat.o \ molval.o \ mullik.o \ mult.o \ nllsq.o \ nuchar.o \ parsav.o \ partxy.o \ pathk.o \ paths.o \ perm.o \ polar.o \ powsav.o \ powsq.o \ prtdrc.o \ quadr.o \ react1.o \ read.o \ reada.o \ refer.o \ repp.o \ rotat.o \ rotate.o \ rsp.o \ search.o \ second.o \ setupg.o \ solrot.o \ swap.o \ symtry.o \ thermo.o \ timer.o \ update.o \ vecprt.o \ write.o \ wrtkey.o \ wrttxt.o \ xyzint.o SRCS = aababc.f \ analyt.f \ anavib.f \ axis.f \ block.f \ bonds.f \ calpar.f \ capcor.f \ chrge.f \ cnvg.f \ compfg.f \ dcart.f \ delmol.f \ delri.f \ denrot.f \ depvar.f \ deriv.f \ ders.f \ dfpsav.f \ diat.f \ diat2.f \ dipind.f \ dipole.f \ dot.f \ drc.f \ drcout.f \ enpart.f \ exchng.f \ ffhpol.f \ flepo.f \ fmat.f \ fock1.f \ force.f \ forsav.f \ frame.f \ freqcy.f \ geout.f \ getgeo.f \ getsym.f \ gmetry.f \ gover.f \ grid.f \ h1elec.f \ haddon.f \ hcore.f \ helect.f \ hqrii.f \ ijkl.f \ interp.f \ iter.f \ linmin.f \ local.f \ locmin.f \ mamult.f \ matout.f \ meci.f \ moldat.f \ molval.f \ mullik.f \ mult.f \ nllsq.f \ nuchar.f \ parsav.f \ paths.f \ perm.f \ polar.f \ powsav.f \ powsq.f \ prtdrc.f \ quadr.f \ react1.f \ read.f \ reada.f \ refer.f \ repp.f \ rotat.f \ search.f \ second.f \ setupg.f \ solrot.f \ swap.f \ symtry.f \ thermo.f \ update.f \ vecprt.f \ write.f \ wrtkey.f \ xyzint.f all: $(PROGRAM) $(PROGRAM): $(OBJS) $(SPECIAL) $(LIBS) @echo -n "Loading $(PROGRAM) ... " @$(LINKER) $(LDFLAGS) $(OBJS) $(SPECIAL) $(LIBS) -o $(PROGRAM) @echo "done" depend:; @mkmf -f $(MAKEFILE) PROGRAM=$(PROGRAM) DEST=$(DEST) dist:; @rdist index:; @ctags -wx $(HDRS) $(SRCS) install: $(PROGRAM) @echo Installing $(PROGRAM) in $(DEST) @install $(PROGRAM) $(DEST) clean: rm -f $(OBJS) $(SPECIAL) lint:; lint ${LINTFLAGS} ${SRCS} print:; @$(PRINT) $(HDRS) $(SRCS) program: $(PROGRAM) tags: $(HDRS) $(SRCS); @ctags $(HDRS) $(SRCS) update: $(DEST)/$(PROGRAM) $(DEST)/$(PROGRAM): $(SRCS) $(LIBS) $(HDRS) $(EXTHDRS) @make -f $(MAKEFILE) DEST=$(DEST) install ### ----------------- Cut Here ------------------------------ Good luck! Yufei Guo email: guo@hyper.com Tel: (519) 725-4040 ******************************************************************************** ******************************************************************************** ******************************************************************************** ******************************************************************************** Dear Kris, Compiling MOPAC for SGI machines First if you have VAX source, you need to convert all the *.FOR filenames to *.f . With MOPAC-6 I have found it easier to handle a single source file so I concatenate all the individual source files:- cat *.f >mopacsgi.f (I suppose you could do:- cat *.FOR >mopacsgi.f ) This makes things easier if you have to make minor modifications to FORMAT atatements etc. since you can search for the part you want to modify more easily. However you do need to make sure that you have enough space in the "tmp" directories. Also I am afraid that I have never been able to understand "makefile's", so I do a simple command line:- f77 -mips2-static -o mopacexe -O2 -Olimit 2000 mopacsgi.f The alternative with individual files is to have a multi-line command:- f77 -mips2 -static -o mopacexe -O2 -Olimit 2000 \ aababc.f \ analyt.f \ . . xyzint.f The list of the files is conveniently got by the command:- ls *.f > filelist Then edit (vi) "filelist" and do:- 1,$ s/.f/.f \/ to put in the backslash characters. Within the compilation command the "-static" command is to ensure that variables are initiallised, and that local variables in a subroutine (i.e. those not declared in COMMON) retain their values from one call of the subroutine to another. The "-O2" level of optimisation is the maximum that can be used. It is best to omit this on a first compilation, so that any errors are found quickly. (Compilation with -O2 takes a lot longer than without it). Only put in the "-mips2" option if you are going to RUN the executable on a "64-bit" machine (R4000, R4600, or R4400). I hope that this helps. Yours sincerely Peter Bladon ******************************************************************************** ******************************************************************************** ******************************************************************************** ******************************************************************************** Dear Kris, The world is small... I have just downloaded Mopac6 from Oakland to my SGI Indy (yesterday !) and encountered exactly the same problem. I have changed Makefile somewhat and, since I do not have Fortran compiler, compiled the whole thing on IRIS Indigo Elan R4000 (Irix 4.0.5F) using f77. The job was done with the inclusion of electrostatic potential option (i.e., I renamed file esp.rof to esp.f and use slightly modified Makefile, included below). The compilation went surprisingly smoothly with only one error: "Error in esp.f: Incompatible lengths for COMMON block WORK1" and this is obvious: the mentioned block in procedure SURFAC in esp.f has one integer array, whereas other procedures use double precision only. I will ask the Mopac author to explain this (do you have his e-mail address ?) Anyway, I have got nice executable version mopacrsm.exe, and so far did test calculations with included 1scf.dat; the results were OK. For practical work on Unix machines you shall use shell script mopac.csh, which is included in the package. Modified Makefile is included below. P.S. 1) I am not a professional programmer and could be wrong. Would you please forward me all answers you will get on this subject ? 2) I am not a quantum chemist either; maybe you know why there are no Mopac parameters for transition metals (especially copper) ? Or, if they exist, where to find them ? +[]={}-()~|+[]={}-()~|+[]={}-()~|+[]={}-()~|+[]={}-()~|+[]={}-()~|+[]={}-()~|+ + |\+_+/\+_+/| + + just Robert Fraczkiewicz |=\ /||\ /=| robert@roman.chem.uh.edu + + Deparment of Chemistry |--\-||-\--| chem86@jetson.uh.edu + + University of Houston |=/_\||/_\=| (713) 743-3236 + + |/+ +\/+ +\| + +[]={}-()~|+[]={}-()~|+[]={}-()~|+[]={}-()~|+[]={}-()~|+[]={}-()~|+[]={}-()~|+ + + + "It is also a good rule not to put too much confidence in experimental + + results until they have been confirmed by Theory" + + + + Sir Arthur Eddington + + + +[]={}-()~|+[]={}-()~|+[]={}-()~|+[]={}-()~|+[]={}-()~|+[]={}-()~|+[]={}-()~|+ From walterse@mis.fuhscms.edu Fri Jul 1 13:04:45 1994 Received: from mis.fuhscms.edu for walterse@mis.fuhscms.edu by www.ccl.net (8.6.9/930601.1506) id MAA11480; Fri, 1 Jul 1994 12:53:10 -0400 Message-Id: <199407011653.MAA11480@www.ccl.net> Subject: CCL:Graduate programs in pharmacognostics? To: chemistry@ccl.net Date: Fri, 1 Jul 1994 12:01:34 -0600 (CST) From: "Dr. D.Eric Walters" X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit Content-Length: 1710 Forwarded message: > On Jul 1, 9:14am, DAVID W. EWING (216) 397-4742 wrote: > > Subject: CCL:Graduate programs in pharmacognostics? > > Since many of you on this list are in the medicinal sciences, perhaps you > > could help me. One of my students is looking for a graduate program in > > pharmacognostics (pharmacognosy). Which schools have such a program? > > I'd advise him to be very careful. This is only one step away from > pharmatheism, and we all know where that leads. :-) > > More seriously, what the hell is (or are) pharmacognostics? I ask > publically, rather than privately, because I suspect that other > inquiring minds might also want to know.... > > -P. > > > -- > ******* After the revolution, everyone will have a home page... ****** > *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* > *New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * > *** ... but the Internet will be too busy for anyone to access it. *** > Pharmacognosy (in Pharmacy School we used to call it "weeds & seeds") is essentially natural product chemistry as it applies to medicinal substances. It used to be all plant stuff, but has been broadened in some schools to include other natural substances, e.g., antibiotics & things from microorganisms. Eric Walters * D. Eric Walters, Ph.D., Associate Professor, Biological Chemistry * Finch University of Health Sciences/The Chicago Medical School * 3333 Green Bay Road, North Chicago, IL 60064 * ph 708-578-3000, x-498;fax 708-578-3240; email: walterse@mis.fuhscms.edu * "A man would do nothing if he waited until he could do it so well that * no one would find fault with what he had done." --Cardinal Newman From burke@agouron.com Fri Jul 1 15:04:53 1994 Received: from agouron.com for burke@agouron.com by www.ccl.net (8.6.9/930601.1506) id OAA13037; Fri, 1 Jul 1994 14:58:15 -0400 Received: from agouron.agouron.com by agouron.com via SMTP (931110.SGI/930901.SGI) for chemistry@ccl.net id AA29217; Fri, 1 Jul 94 11:57:25 -0700 Received: by agouron (5.64/10.0) id AA23070; Fri, 1 Jul 94 11:57:23 -0700 Date: Fri, 1 Jul 94 11:57:23 -0700 From: burke@agouron.com (Ben Burke) Message-Id: <9407011857.AA23070@agouron> To: EWING@jcvaxa.jcu.edu, chemistry@ccl.net, shenkin@columbia.edu Subject: CCL:ANS:Pharmacognosy ewing@jcvaxa.jcu.edu wrote: >Since many of you on this list are in the medicinal sciences, perhaps you >could help me. One of my students is looking for a graduate program in >pharmacognostics (pharmacognosy). Which schools have such a program? >Thank you for any suggestions you might have. Further, Peter Shenkin (shenkin@columbia.edu) wrote: >More seriously, what the hell is (or are) pharmacognostics? In reverse order, Pharmacognosy is the study of pharmaceuticals from plant sources. Researchers investigate folklore and interview persons who use plants for medicinal purposes. Based on this data, researchers collect, identify, and catalog plants which are indicated for medicinal uses. Often these are places like rainforests, and people like shamans. Extracts of the plants are tested in screens related to the medicinal activity claimed. Fractionation is continued until the active components are isolated, purified and characterized. These components either become drugs themselves, or become new leads for drugs. Of course, many of the drugs we use today are isolated from plant sources or are semi-synthetic versions of the same. We all can appreciate the example that aspirin comes from willow bark (Chinese remedy). [Peter: As an aside: Perhaps talk with Koji Nakanishi. He spoke at a graduate-student-organized meeting for a consortium of Midwest schools with programs of Med Chem/Pharmacognosy (in Chicago in 1990).] In particular, I would suggest a look at the University of Illinois at Chicago. They have a program in pharmacognosy that is extensive and well respected throughout the world. Some of the top scholars in the field are concentrated there, and Chicago is a great city. And being in Chicago allows them access to incredible facilities (like the Field Museum for plant identification, etc.). Researchers there also have a close association with World Health Organization. Try: Dept of Medicinal Chemistry and Pharmacognosy, Mail Code 781, 833 S. Wood Street, Chicago IL 60612 or call: 312-996-7245 (department head, main office) For protocol's sake: They also train computational chemists at UIC. Best to you, -Ben Burke (graduate of UIC Med Chem Dept) burke@agouron.com Agouron Pharmaceuticals As usual, these are my opinions and not those of Agouron Pharmaceuticals. From waller@thor.herl.epa.gov Fri Jul 1 16:04:46 1994 Received: from thor.herl.epa.gov for waller@thor.herl.epa.gov by www.ccl.net (8.6.9/930601.1506) id PAA13685; Fri, 1 Jul 1994 15:34:26 -0400 Received: by thor.herl.epa.gov (931110.SGI/1.34) id AA01004; Fri, 1 Jul 94 15:35:03 -0400 From: "Chris L. Waller" Message-Id: <9407011535.ZM1002@thor.herl.epa.gov> Date: Fri, 1 Jul 1994 15:35:03 -0400 In-Reply-To: "Peter Shenkin" "CCL:Graduate programs in pharmacognostics?" (Jul 1, 11:00am) References: <01HE6Q6CX69E8WWKL3@jcvaxa.jcu.edu> <9407011100.ZM16942@still3.chem.columbia.edu> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "Peter Shenkin" , chemistry@ccl.net, EWING@jcvaxa.jcu.edu Subject: Re: CCL:Graduate programs in pharmacognostics? Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 >From Tabor's Cyclopedic Medical Dictionary: pharmacognosy - the science of natural drugs and their physical, botanical, and chemical properties. That being the case, I guess the UNC School of Pharmacy has a program in the Division of Medicinal Chemistry and Natural Products. With regard to Natural Products, I suppose the contact person would be K. H. Lee. One could speak with Steven D. Wyrick (Acting Chairman) about the Program in general. Chris ******************************************************************** *Chris L. Waller, Ph.D. PHONE 919-541-7976* *Research Chemist FAX 919-541-5394* *waller@thor.herl.epa.gov * *Pharmacokinetics Branch (MD-74) * *ETD/HERL/USEPA * *Research Triangle Park, NC 27711 * * * *Disclaimer: Mention of trade names or products does not constitute* *endorsement by the United States Environmental Protection Agency. * ******************************************************************** From chemdcl3@emrycc.cc.emory.edu Fri Jul 1 17:04:48 1994 Received: from emoryu1.cc.emory.edu for chemdcl3@emrycc.cc.emory.edu by www.ccl.net (8.6.9/930601.1506) id QAA14402; Fri, 1 Jul 1994 16:48:35 -0400 Received: from emrycc.cc.emory.edu by emoryu1.cc.emory.edu (5.65/Emory_cc.3.5.2) via SMTP id AA13606 ; Fri, 1 Jul 94 16:48:33 -0400 Message-Id: <9407012048.AA13606@emoryu1.cc.emory.edu> Date: 1 Jul 94 16:48:00 EST From: "DR. LIOTTA" Subject: CCL:Ribosomal RNA To: "chemistry" We would like to model the secondary structure of ribosomal RNA and would like to contact anybody who has done similar work or who can lead us to useful references. Are there any crystollographic structures of ribosomal RNA available? Thank you, V.Cornel, chemdcl3@emrycc.cc.emory.edu From rickr@scripps.edu Fri Jul 1 17:07:36 1994 Received: from scripps.edu for rickr@scripps.edu by www.ccl.net (8.6.9/930601.1506) id QAA14267; Fri, 1 Jul 1994 16:33:11 -0400 Received: from ppg.scripps.edu by scripps.edu (5.61/1.34) id AA05984; Fri, 1 Jul 94 13:33:08 -0700 Received: by ppg.Scripps.EDU (4.1/SMI-4.1/TSRI1.0) id AA07440; Fri, 1 Jul 94 13:18:13 PDT Date: Fri, 1 Jul 94 13:18:13 PDT From: rickr@scripps.edu (Rick Ross) Message-Id: <9407012018.AA07440@ppg.Scripps.EDU> To: chemistry@ccl.net Subject: DFT_symposium CALL FOR PAPERS DENSITY FUNCTIONAL THEORY IN CHEMISTRY Including electronic structure and statistical mechanics methodology and applications April 2 - April 7 Spring 1995 American Chemical Society National Meeting Anaheim, CA Both poster and oral contributions will be accepted. Authors should indicate their choice. The number of oral contributions is limited. Contributions not placed in oral sessions will be placed in the poster session. Cosponsored by the Divisions of Computers in Chemistry and Physical Chemistry Send abstracts on official ACS forms (available from organizers) to: Professor Brian Laird, Department of Chemistry, The University of Kansas, Lawrence, Kansas USA 66045-0046 (913) 864-4632 laird@pilsner.chem.ukans.edu or Dr. Rick Ross, PPG Industries, P.O. Box 9, Allison Park, PA USA 15101 (412) 492-5359; rickr@ppg.scripps.edu or Professor Tom Ziegler, Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 1N4 (403) 220-5368 ziegler@zinc.chem.ucalgary.ca ***** DEADLINE FOR ABSTRACTS: OCTOBER 29, 1994 ***** From rickr@scripps.edu Fri Jul 1 17:10:21 1994 Received: from scripps.edu for rickr@scripps.edu by www.ccl.net (8.6.9/930601.1506) id QAA14251; Fri, 1 Jul 1994 16:32:12 -0400 Received: from ppg.scripps.edu by scripps.edu (5.61/1.34) id AA05950; Fri, 1 Jul 94 13:32:08 -0700 Received: by ppg.Scripps.EDU (4.1/SMI-4.1/TSRI1.0) id AA07435; Fri, 1 Jul 94 13:17:12 PDT Date: Fri, 1 Jul 94 13:17:12 PDT From: rickr@scripps.edu (Rick Ross) Message-Id: <9407012017.AA07435@ppg.Scripps.EDU> To: chemistry@ccl.net Subject: DFT_symposium CALL FOR PAPERS DENSITY FUNCTIONAL THEORY IN CHEMISTRY Including electronic structure and statistical mechanics methodology and applications April 2 - April 7 Spring 1995 American Chemical Society National Meeting Anaheim, CA Both poster and oral contributions will be accepted. Authors should indicate their choice. The number of oral contributions is limited. Contributions not placed in oral sessions will be placed in the poster session. Cosponsored by the Divisions of Computers in Chemistry and Physical Chemistry Send abstracts on official ACS forms (available from organizers) to: Professor Brian Laird, Department of Chemistry, The University of Kansas, Lawrence, Kansas USA 66045-0046 (913) 864-4632 laird@pilsner.chem.ukans.edu or Dr. Rick Ross, PPG Industries, P.O. Box 9, Allison Park, PA USA 15101 (412) 492-5359; rickr@ppg.scripps.edu or Professor Tom Ziegler, Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 1N4 (403) 220-5368 ziegler@zinc.chem.ucalgary.ca ***** DEADLINE FOR ABSTRACTS: OCTOBER 29, 1994 ***** From jkl@ccl.net Fri Jul 1 18:04:48 1994 Received: from krakow.ccl.net for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id RAA15127; Fri, 1 Jul 1994 17:33:53 -0400 From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.6.9/920428.1525) id RAA06370; Fri, 1 Jul 1994 17:33:51 -0400 Date: Fri, 1 Jul 1994 17:33:51 -0400 Message-Id: <199407012133.RAA06370@krakow.ccl.net> To: chemistry@ccl.net Subject: List will be sick on the weekend Cc: jkl@ccl.net Dear Netters, This is your CCL coordinator speaking. I am back after wandering for over 3 weeks and I am trying to catch up --- actually I was trying unsuccessfully to catch up before I left... Over the long weekend, our system people will be upgrading, changing and extending. Simply, messing up. So please refrain from using CCL, since the results may not be predictable. For US subscribers it may be actually easy (have a nice holiday and watch the fireworks!!!). For others, please bear with us, and even if you do not like "America, the beautiful", take into account that some of us have a hard time here too (viz. Bob Clinton trying to prove that he is not that mucho) and you will relax. Jan jkl@ccl.net From raman@bioc01.uthscsa.edu Fri Jul 1 19:04:47 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.9/930601.1506) id SAA15760; Fri, 1 Jul 1994 18:47:20 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Fri, 1 Jul 1994 17:50:08 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA10854; Fri, 1 Jul 94 17:47:41 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9407012247.AA10854@bioc01.uthscsa.edu> Subject: Re: CCL:Ribosomal RNA To: chemdcl3@emrycc.cc.emory.edu (DR. LIOTTA) Date: Fri, 1 Jul 1994 17:47:41 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <9407012048.AA13606@emoryu1.cc.emory.edu> from "DR. LIOTTA" at Jul 1, 94 04:48:00 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 3042 Hi: > We would like to model the secondary structure of ribosomal > RNA and would like to contact anybody who has done similar > work or who can lead us to useful references. Are there any > crystollographic structures of ribosomal RNA available? To the best of my knowledge there are two items in the PDB that might interest you: (a) theoretical model of 5s rRNA and (b) NMR structures of rRNA. Here are the headers for your information: HEADER RIBONUCLEIC ACID 23-JUN-93 1ELH COMPND 5S RIBOSOMAL RNA (HELIX I) (NMR, 6 STRUCTURES) SOURCE (ESCHERICHIA COLI) EXPDTA NMR AUTHOR S.WHITE,P.MOORE REVDAT 1 31-JAN-94 1ELH 0 JRNL AUTH S.A.WHITE,M.NILGES,A.HUANG,A.T.BRUNGER,P.B.MOORE JRNL TITL NMR ANALYSIS OF HELIX I FROM THE 5S RNA OF JRNL TITL 2 ESCHERICHIA COLI JRNL REF BIOCHEMISTRY V. 31 1610 1992 JRNL REFN ASTM BICHAW US ISSN 0006-2960 033 ######################################################################## HEADER RIBONUCLEIC ACID 22-JUN-91 1RRN COMPND 5 S RIBOSOMAL RNA (THEORETICAL MODEL) SOURCE (XENOPUS LAEVIS) OOCYTES EXPDTA THEORETICAL MODEL AUTHOR E.WESTHOF,P.ROMBY,C.EHRESMANN REVDAT 2 31-JAN-94 1RRNA 1 REMARK REVDAT 1 31-OCT-93 1RRN 0 JRNL AUTH E.WESTHOF,P.ROMBY,P.J.ROMANIUK,J.-*P.EBEL, JRNL AUTH 2 C.EHRESMANN,B.EHRESMANN JRNL TITL COMPUTER MODELING FROM SOLUTION DATA OF SPINACH JRNL TITL 2 CHLOROPLAST AND OF XENOPUS LAEVIS SOMATIC AND JRNL TITL 3 OOCYTE 5 S $R/RNA$S JRNL REF J.MOL.BIOL. V. 207 417 1989 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 070 Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From jomal@dfq.ufrj.br Fri Jul 1 21:04:54 1994 Received: from chopin.dfq.ufrj.br for jomal@dfq.ufrj.br by www.ccl.net (8.6.9/930601.1506) id UAA16399; Fri, 1 Jul 1994 20:35:27 -0400 Received: (jomal@localhost) by chopin.dfq.ufrj.br (8.6.9/8.3) id VAA16892; Fri, 1 Jul 1994 21:35:54 GMT Date: Fri, 1 Jul 1994 21:35:54 GMT From: "Joao Otavio M.A. Lins / DFQ-IQ-UFRJ" Message-Id: <199407012135.VAA16892@chopin.dfq.ufrj.br> To: chemistry@ccl.net Subject: 3d-editor Dear netters, I'm looking for a free/PD 3D molecular editor. This editor can be even a starting point since my idea is to modify it and insert it into a good PD molecular graphics program. Any hints? Thanks in advance, Joao O.M.A. Lins Quantum Chemistry Group ______________________________________________________________________ Instituto de Quimica da U.F.R.J. email: jomal@dfq.ufrj.br Centro de Tecnologia, bloco A, sala 412 voice: +55-21-590-9890 Cidade Universitaria fax : +55-21-290-4746 21949-900 - Rio de Janeiro - RJ BRAZIL ______________________________________________________________________