From Leif.Laaksonen@pobox.csc.fi Wed Apr 13 01:12:19 1994 Received: from pobox.csc.fi for Leif.Laaksonen@pobox.csc.fi by www.ccl.net (8.6.4/930601.1506) id BAA19638; Wed, 13 Apr 1994 01:07:02 -0400 Received: from [128.214.46.163] (laaksone.csc.fi) by pobox.csc.fi with SMTP id AA12389 (5.65c8+/IDA-1.4.4 for ); Wed, 13 Apr 1994 08:06:58 +0300 Date: Wed, 13 Apr 1994 08:06:58 +0300 Message-Id: <199404130506.AA12389@pobox.csc.fi> X-Sender: laaksone@finsun.csc.fi Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: Leif.Laaksonen@csc.fi Subject: CCL:Looking for RMS distance calculator On Apr 11, 12:56pm, Luca Jovine wrote: > Subject: CCL:Looking for RMS distance calculator > > Dear Netters, > > I am looking for a program that could calculate a RMS distance matrix > for a set of homologous molecular structures (possibly in PDB format). > It would be even better if such program allowed to pick which parts of > the structures to compare.... The program SCARECROW has also a facility to calculate a RMS distance matrix for a set of molecular structures. It is possible to display the result on the screen of a SGI machine or write it to disk. The user can choose the atoms to include in the comparison list. I have used it a bit in a crude cluster analysis approach. For more information about SCARECROW look at: URL: http://www.csc.fi/lul/chem/scarecrow/jmg_scare.html The program is still available from nic.funet.fi using the anonymous ftp account from directory pub/sci/chem/scarecrow. Cheers, -leif laaksonen ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 0 4572378 P.O. Box 405 | Telefax: 358 0 4572302 FIN-02101 Espoo | Voice Mail: 358 486257407 FINLAND | Mail: Leif.Laaksonen@csc.fi --------URL: http://www.csc.fi/lul/leif/leif.laaksonen.html-------- New opinions are always suspected, and usually opposed, without any other reason but because they are not already common. John Locke ------------------------------------------------------------------- From chris@glycob.ox.ac.uk Wed Apr 13 11:12:28 1994 Received: from oxglua for chris@glycob.ox.ac.uk by www.ccl.net (8.6.4/930601.1506) id LAA25424; Wed, 13 Apr 1994 11:09:10 -0400 From: Received: by glycob.ox.ac.uk (MX V3.1C) id 18244; Wed, 13 Apr 1994 15:59:27 EDT Date: Wed, 13 Apr 1994 15:59:25 EDT To: chemistry@ccl.net Message-ID: <0097CE6E.8ABBD8C0.18244@glycob.ox.ac.uk> Subject: Biophysical Society workshop Sorry to occupy bandwidth but could anyone tell me where I could contact the organizer of the workshop held by the Biophysical Society on March 6-10 in Louisianaon the topic of Molecular Aspects of carbohydrate interaction on Membrane Surfaces? I would be interested in obtaining the proceedings. Thank you *************************************************************** * Dr. Chris. Edge * Tel. +44-865-275-338 * * Glycobiology Institute * Fax. +44-865-275-216 * * Oxford University * e-mail chris@glycob.ox.ac.uk * * South Parks Road * 100117.3646@compuserve.com * * Oxford OX1 3QU U.K. * * *************************************************************** From h.rzepa@ic.ac.uk Wed Apr 13 11:47:44 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id LAA25415; Wed, 13 Apr 1994 11:07:59 -0400 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <26532-0@punch.ic.ac.uk>; Wed, 13 Apr 1994 16:06:52 +0100 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA19899; Wed, 13 Apr 94 16:07:19 +0100 Message-Id: <9404131507.AA19899@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@sg1.cc.ic.ac.uk Return-Receipt-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 13 Apr 1994 15:07:00 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: WWW94 and chemistry Cc: Ibrahim Bertrand To the OSC Mail Exploder: The first www conference is being organised on 25-27 May at CERN in Switzerland. A series of workshops are being organised for specialist subject disciplines. I have proposed a workshop on the use of WWW for Chemistry, and have been designated its coordinator. To see the current list, connect to http://cui_www.unige.ch/WWW94/Workshops/workshop.list.html and for my "position paper" connect to; http://cui_www.unige.ch/WWW94/Workshops/Rzepa.Henry.position.html I am hoping that at least two or three others may wish to make contributions to this workshop. If you are interested, either mail Ibrahim Bertrand or me, preferably enclosing a short discussion paper in "html" format, which will be mounted at the www server. If you wish to register for www94, go to http://www1.cern.ch/WWW94/Registration.html (it can be done with a "form" and credit card there and then! Now thats the way to organise a conference! ACS and RSC are you listening?) Whilst attendance is desirable if your contribution is more than a comment (after all I do not want to hold a workshop just with myself) some contributions "without attendance" could be accepted (Ibrahim Bertrand is the final arbitor on this!) This venue also offers an chance to find out the directions of www development, and perhaps even influence the directions it goes in! Chemists have been thoroughly left behind by the molecular biologists, and we must catch up! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.02, Tel:+44 71 225 8339, Fax:+44 71 589 3869. >From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804 http://www.ch.ic.ac.uk/rzepa.html From tom@sgih.roc.wayne.edu Wed Apr 13 14:12:44 1994 Received: from rocdec.roc.wayne.edu for tom@sgih.roc.wayne.edu by www.ccl.net (8.6.4/930601.1506) id OAA28102; Wed, 13 Apr 1994 14:03:45 -0400 Received: by rocdec.roc.wayne.edu (5.57/Ultrix3.0-C) id AA05781; Wed, 13 Apr 94 13:59:39 -0400 Received: from TomsPowerBook.roc.wayne.edu by sgih.roc.wayne.edu via SMTP (920110.SGI/890607.SGI) (for @rocdec.roc.wayne.edu:chemistry@ccl.net) id AA03619; Wed, 13 Apr 94 14:04:14 -0400 Date: Wed, 13 Apr 94 14:04:14 -0400 Message-Id: <9404131804.AA03619@sgih.roc.wayne.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: tom@sgih.roc.wayne.edu (Tom Wiese) Subject: AM1 vs PM3 Charges in CoMFA? Hello Netters, I just read Dr. Holders comments about AM1 vs PM3. What caught my interest the most was that part about PM3 charges being "unreliable". I would like to hear comments from those in the know as to which method of generating charges, AM1 vs PM3, contributes to better/more useful CoMFA models? We have been using PM3 to generate structures and charges for various steroidal estrogens that are used ultimately in CoMFA. Compared to X-ray data, we found that PM3 gives slightly better geometry than AM1 for typical estrogens (Thomas E. Wiese and S. C. Brooks, "Molecular Modeling of Steroid Estrogens: Novel Conformations and Their Role in Biological Activity" in The Journal of Steroid Biochemistry and Molecular Biology, In Press). However, we found AM1 to give very poor geometry of nitro and amino substituted estrogen analogues when compared to PM3. So, to be consistent, we used PM3 for all compounds in the data set and have generated useful CoMFA models. I would also like to know if some body out there has a comment about CoMFA's generated using geometry from PM3 and charges from AM1? Thanks, Tom ################################################## Tom Wiese Brooks Group Department of Biochemistry Wayne State University School of Medicine 540 E. Canfield Detroit, MI 48201 Phone: (313) 577-5605 FAX: (313) 577-2765 email: tom@sgih.roc.wayne.edu ################################################## ################################################## From jle@world.std.com Wed Apr 13 16:12:36 1994 Received: from news.std.com for jle@world.std.com by www.ccl.net (8.6.4/930601.1506) id QAA29812; Wed, 13 Apr 1994 16:05:38 -0400 Received: from world.std.com by news.std.com (5.65c/Spike-2.1) id AA14986; Wed, 13 Apr 1994 16:04:29 -0400 Received: by world.std.com (5.65c/Spike-2.0) id AA12882; Wed, 13 Apr 1994 16:04:20 -0400 Date: Wed, 13 Apr 1994 16:04:20 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199404132004.AA12882@world.std.com> To: chemistry@ccl.net Subject: Semi-empirical parameterization... Something for folks to think about... The various SE parameter sets were all (to the best of my knowledge) developed on VAXen about 10-ish years ago (6-ish for PM3?). Since that time, there's been a 2-4 orders-of-magnitude increase in CPU horsepower, and there has to be an improvement in the quality and/or amount of experimental data to parameterize against. Doesn't this suggest that it's a worthwhile idea to develop an AM2/PM4 set (with or without d-orbitals) that could (a) use the extra stuff mentioned above and (b) specifically examine the known problem areas of the various methods? Judging from solvation work such as AMSOL, parameter sets can be generated in a CPU-day or a CPU-week on the high-end stuff available now. Several/Many sets of params can be generated very quickly, using whatever scientific or empirical constraints one wishes to impose... This doesn't even take "novel" machines like SIMD/MIMD/MPP boxes into account - these might make the process even faster. Folks will probably say that "we should not invalidate past results". True, but if Allinger's allowed three different mechanics FF's (not counting the modifications to each that have appeared over time), I think folks will readily accept a new SE parameter set if it's properly done and disseminated. This way, we'll be able to get rid of any problem areas that are artifacts of the limited capabilities and/or datasets used in the earlier work. It will also let folks include LARGE small molecules as opposed to the SMALL small molecules used in the past. Whatcha think? Joe Leonard jle@world.std.com From tudor@wucmd.wustl.edu Wed Apr 13 16:15:30 1994 Received: from wugate.wustl.edu for tudor@wucmd.wustl.edu by www.ccl.net (8.6.4/930601.1506) id PAA29346; Wed, 13 Apr 1994 15:24:10 -0400 Received: by wugate.wustl.edu (5.67b+/WUSTL-0.3) with SMTP id AA24748; Wed, 13 Apr 1994 14:24:07 -0500 Received: by wucmd (920330.SGI/911001.SGI) for @wugate.wustl.edu:chemistry@ccl.net id AA03851; Wed, 13 Apr 94 13:21:28 -0500 Date: Wed, 13 Apr 1994 13:08:32 -0500 (CDT) From: Tudor Oprea Subject: Re: CCL:AM1 vs PM3 Charges in CoMFA? To: Tom Wiese Cc: chemistry@ccl.net In-Reply-To: <9404131804.AA03619@sgih.roc.wayne.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In my opinion, using one hamiltonian or the other is just a method to achieve internally consistent models, and cross-validation is a mere test of the internal consistency (or robustness). As such, i do not think it is hamiltonian dependent - after all, there are CoMFA models relying on AM1 optimized geometries as well. As long as you are consistent for all the training set with the charge-set and geometry, your correlation should hold true for both AM1 and PM3, once the successful alignment rule has been discovered. With respect to charges, using AM1 vs PM3 should not yield a significant difference (e.g., more than .2 in cross-validated r^2), and if it does, that model becomes a problem (likely to be a spurious correlation). Whatever differences in charges are observed at, e.g., nitrogen atoms, unless those charges are really important for biological activity, you are likely to get similar regression analyses. After all, they would both be models, not necesarrily reflecting the exact physico-chemical reality. I do not exclude the possibility that, for some training sets, the PM3 charge / geometry model to be significantly better (or worse) than its AM1 counterpart, but I doubt that such findings would be general. --Tudor ========================== Tudor-Ionel Oprea = Tel. (1-314) 935 4672 = Research Associate = Fax. (1-314) 935 4979 = Washington University Center for Molecular Design = Email: = Lopata 510, Box 1099, One Brookings Drive = tudor@wucmd.wustl.edu = St.Louis MO 63130 ========================== From C1790@SLVAXA.UMSL.EDU Wed Apr 13 17:12:35 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.4/930601.1506) id QAA00816; Wed, 13 Apr 1994 16:46:27 -0400 From: Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.2-11 #2503) id <01HB4QWT2AS09ZMG46@SLVAXA.UMSL.EDU>; Wed, 13 Apr 1994 15:46:59 CST Date: Wed, 13 Apr 1994 15:46:59 -0600 (CST) Subject: CENTRAL RESOURCE FOR COMPUTATIONAL-CHEMISTRY FILMS/VIDEO To: CHEMISTRY@ccl.net Message-id: <01HB4QWT2U2Q9ZMG46@SLVAXA.UMSL.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT DEAR NETTERS, IS ANYONE AWARE OF ANY (CENTRAL) RESOURCES FOR OBTAINING FILMS/VIDEO ON RELATED TOPICS SUCH AS COMPUTATIONAL CHEMISTRY, MOLECULAR COMPUTER GRAPHICS , ETC.? FOR EXAMPLE, I ONCE SAW A VIDEO AT A GORDON CONFERENCE (ON COMPUT. CHEM.) WHICH VISUALIZED A CHEMICAL REACTION AS SIMULATED BY AM1 'REACTION COORDINATE'. MANY OTHER PEOPLE HAVE INTERESTING MOLECULAR DYNAMICS SIMULATIONS THAT HAVE BEEN CAPTURED ON VIDEO FILM. IF THIS IDEA MAKES SENSE, CAN SOMEONE SUGGEST A GOOD LOCATION THAT WOULD SERVE AS A CENTRAL RESOURCE (e.g., QCPE?). THANKS .... BILL WELSH DEPT. OF CHEMISTRY UNIV. OF MISSOURI-ST. LOUIS From RONSAUERS@rutchm.rutgers.edu Wed Apr 13 17:13:51 1994 Received: from RUTCHM.RUTGERS.EDU for RONSAUERS@rutchm.rutgers.edu by www.ccl.net (8.6.4/930601.1506) id QAA00634; Wed, 13 Apr 1994 16:27:54 -0400 Date: Wed, 13 Apr 1994 16:27 EST From: RRS Subject: Triplet carbonyls by MINDO/3 To: CHEMISTRY@ccl.net Message-id: <726F91F8B4C06537@rutchm.rutgers.edu> X-Organization: Department of Chemistry at Rutgers University X-Envelope-to: CHEMISTRY@ccl.net X-VMS-To: IN%"CHEMISTRY@ccl.net" Netters: We have just completed a fairly detailed series of computations of triplet state geometry and energy of formaldehyde and butanal by both ab initio (UMP2/6-311+G**) and UHF semi-empirical methods (AM1, PM1, MINDO/3, and MNDO). We are struck by the finding that only MINDO/3 reproduces the non-planar structure (out-of-plane angles are ca. 40+ degrees) of the lowest triplet state of these molecules that one gets from ab initio methodology and from experimental determinations. Can anyone explain why only MINDO/3 gives rise to the non-planar geometry and not the other semi-empirical methods? I will post summaries of the answers. Thanks, RRSauers From burkhart@goodyear.com Wed Apr 13 18:12:34 1994 Received: from goodyear.com for burkhart@goodyear.com by www.ccl.net (8.6.4/930601.1506) id RAA01619; Wed, 13 Apr 1994 17:43:02 -0400 Received: from rdsrv2 (rdsrv2.goodyear.com) by goodyear.com (4.1/SMI-4.1) id AA10995; Wed, 13 Apr 94 17:43:01 EDT Received: from rds325 by rdsrv2 (4.1/SMI-4.1) id AA05151; Wed, 13 Apr 94 17:43:01 EDT Received: by rds325 (920330.SGI/920502.SGI.AUTO) for @rdsrv2:chemistry@ccl.net id AA06313; Wed, 13 Apr 94 17:43:00 -0400 Date: Wed, 13 Apr 94 17:43:00 -0400 From: burkhart@goodyear.com (Craig W. Burkhart) Message-Id: <9404132143.AA06313@rds325> To: chemistry@ccl.net Subject: RE: Semi-empirical parameterization... Netters... I think it is about time that the "semi-empirical" parameter sets be opened up. Joe Leonard makes a very strong case regarding the ability to use larger parameter sets and larger small molecules. I would also suspect that a better set of experimental data could be used--for example, the use of molecular dipoles, etc. are next to worthless in computing heats of reactions, so why use them in the parameter set? This whole field has been closed for a long time. The recent remarks regarding AM1 - PM3 show how one camp can complain about the splinter in someone else's eye while neglecting the large piece of lumber in their own. A good honest discussion of parameterization sets and a forthright, open attempt to better the methods is called for. Thanks to Joe Leonard for having the guts to suggest a worthy proposal. -------------------------------------------------------------------------- Craig W. Burkhart, Ph.D. Senior Research Chemist E-mail: cburkhart@goodyear.com The Goodyear Tire & Rubber Co. Fone: 216.796.3163 Research Center Fax: 216.796.3304 142 Goodyear Boulevard Akron, OH 44305 -------------------------------------------------------------------------- For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled - Feynman -------------------------------------------------------------------------- From cramer@maroon.tc.umn.edu Wed Apr 13 18:14:05 1994 Received: from maroon.tc.umn.edu for cramer@maroon.tc.umn.edu by www.ccl.net (8.6.4/930601.1506) id RAA01611; Wed, 13 Apr 1994 17:42:24 -0400 From: Received: by maroon.tc.umn.edu; Wed, 13 Apr 94 16:25:57 -0500 Message-Id: <0012dac6365a10825@maroon.tc.umn.edu> Subject: Re: CCL:Semi-empirical parameterization... To: jle@world.std.com (Joe M Leonard) Date: Wed, 13 Apr 1994 16:25:57 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <199404132004.AA12882@world.std.com> from "Joe M Leonard" at Apr 13, 94 04:04:20 pm X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 2467 > > Doesn't this suggest that it's a worthwhile idea to develop an AM2/PM4 > set (with or without d-orbitals) that could (a) use the extra > stuff mentioned above and (b) specifically examine the known problem > areas of the various methods? Judging from solvation work such > as AMSOL, parameter sets can be generated in a CPU-day or a CPU-week > on the high-end stuff available now. > It is quite flattering to be held up as an example of fast, effective semiempirical parameterization! In all fairness, however, the SMx solvent models are probably slightly more simple to develop than a full-blown semiempirical parameter set that is designed to reproduce many different chemical properties (not just solvation free energy). [I do not necessarily speak for our entire group in this matter, but I personally believe this to be true.] This is not to suggest that the above is not a laudable goal! It strikes me, though, that more careful evaluation of MNDO/D, SAM1, and SINDO (Thiel et al., Dewar et al., and Jug et al., respectively) would perhaps save some effort in this regard. Regrettably, for a variety of reasons, there appears to be little movement in this direction [Perhaps that should be taken as a compliment to AM1 and PM3]. I suspect that improving on previous Hamiltonians will require a new MODEL, as opposed to another search of parameter space. On another note, ab initio theories are of great value because they are completely general, but the focus of modern chemistry is not completely general. Rather, societal and governmental priorities dictate more pronounced emphasis on specific topics. I wonder if another completely general semiempirical parameterization is really worth the effort. Something that would arguably be better received would be a particularly accurate model for proteins, membranes, [insert your favorite chemical topic here], etc., where the cost function used in the parameterization would be more tightly focused than has been the case in the past. Much like molecular mechanics, such a model would be particularly good at what it is particularly good at, and no guarantees would be offered for distant extensions. Finally, work does continue on semiempirical methods -- they are called exchange-correlation functionals . . . CJC -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 (612) 624-0859 cramer@maroon.tc.umn.edu From SBOESCH@aardvark.ucs.uoknor.edu Wed Apr 13 20:12:32 1994 Received: from aardvark.ucs.uoknor.edu for SBOESCH@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.4/930601.1506) id UAA02817; Wed, 13 Apr 1994 20:11:27 -0400 From: Message-Id: <199404140011.UAA02817@www.ccl.net> Date: Wed, 13 Apr 94 19:11 CDT Subject: running g92 on nqs To: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Dear Netters, I recently installed NQS on our RISC/6000. We also have Gaussian 92. The problem is that only root can run a gaussian job using NQS. If I submit a job as root, the job will run successfully. However, if I submit a job as any other user, the job will not run. I get the following error Warning: no access to tty; thus no job control in this shell... Does anyone have any ideas as to what to do? I would appreciate it if someone who is running NQS and G92 would get in touch with me. Thank you very much. Scott E. Boesch Department of Chemistry & Biochemistry University of Oklahoma Norman, OK 73019 From mw@crystal.uwa.edu.au Wed Apr 13 22:12:34 1994 Received: from uniwa.uwa.edu.au for mw@crystal.uwa.edu.au by www.ccl.net (8.6.4/930601.1506) id VAA03583; Wed, 13 Apr 1994 21:52:13 -0400 Received: from graf.crystal.uwa.edu.au (graf.crystal.uwa.edu.au [130.95.232.1]) by uniwa.uwa.edu.au (8.6.8/8.6.4) with SMTP id JAA11883 for ; Thu, 14 Apr 1994 09:51:35 +0800 Received: from pack.crystal.uwa.edu.au by graf.crystal.uwa.edu.au with SMTP (5.61+IDA+MU) id AA02843; Thu, 14 Apr 1994 10:42:44 +0800 From: mw@crystal.uwa.edu.au (Magda Wajrak) Message-Id: <9404140144.AA03819@pack.crystal.uwa.edu.au> Subject: Barium basis set? To: CHEMISTRY@ccl.net Date: Thu, 14 Apr 94 9:44:27 WST Mailer: Elm [revision: 70.85] Dear Netters, I just wanted to ask if anyone could direct me to a reference or possibly email me a DZP-type basis set for Barium. I have looked in the Poirier book but they don't have any Barium basis sets, although they have just about every basis set. Thank you in advance. Magda Wajrak (mw@crystal.uwa.edu.au)