From BALLY@CFRUNI52.bitnet Mon Jun 27 03:03:34 1994 Received: from CEARN.cern.ch for BALLY@CFRUNI52.bitnet by www.ccl.net (8.6.9/930601.1506) id CAA09228; Mon, 27 Jun 1994 02:51:12 -0400 Message-Id: <199406270651.CAA09228@www.ccl.net> Received: from CFRUNI52.BITNET by CEARN.cern.ch (IBM VM SMTP V2R2) with BSMTP id 7878; Mon, 27 Jun 94 08:48:01 SET Date: Mon, 27 Jun 94 08:50 N From: Subject: structuring CCL! To: CHEMISTRY@ccl.net X-Original-To: CHEMLIST, BALLY Dear netters, As an appendix to his "self-reply" to the question of CI-coeffcients, Aiaz Bakassov made a very valuable suggestion: > I have a suggestion. Why won't all of us who run G92 start their postings > about G92 with keyword "G92" in the beginning of the subject ? This would > make life a bit easier for G92 users. > More generally, if a question is about some software, why don't we always > start the subject from the name of the software?! In filling out the survey on CCL by Alejandro Pisanty I wrote among other things: > As an example, I would find it *extremely* useful to have > lists which deal solely with individual quantum chemistry pro- > grams such as Gaussian, GAMESS etc. The Gaussian help service > is essentially useless unless you pay the $5000 annual mainte- > nance fee and *very many* people out there have questions about > how to do this or that with Gaussian, many of which are trivial > to answer for someone who has gone through the same experience > and has solved the problem. Much of this is now already happening > in CCL but it is buried in lots of "noise". The same is true > of other programs such as GAMESS and I am sure Mike Schmidt would > be extremely grateful if he would not have to answer all the mail > with questions on this program. > Also, questions like "what is the best model/program to solve > this or that problem" could be posed in a dedicated list. I would > be much more ready to contribute answers if I would no longer be > forced to dig out the questions from a mess of completely different > things (some of which may also be interesting to me, but again > only if they are properly classified) I am convinced that CCL *direly* needs some structuring or it will soon become unmanageable for people who cannot afford to spend ours on end with it every day. This structuring is neither obvious nor easy, and it will have to be done *very* thoughfully or otherwise much useful information will wasted. Bakassov's above suggestion would be one way to do it, but I am afraid that eventually this would result in a procrastination of the "Subject:" field which already now starts with "CCL:". If you have to add the name of a quantum chemical program to this, there remains little space to say what the contribution is actually concerned with (I understand that the field may actually be almost as long as you wish, but most mailing software only show the first 25-30 characters and you only get to see the rest when you actually go an open the message). Thus I think sub-lists would be the way to go, although a combination of the above two approaches are also imagineable. What does everybody else out there think about this matter? Why don't you post your proverbial 2 cents worth under the "Subject:" heading "structuring CCL", so we all immediately see what we are dealing with with a toast to the survival of a healthy (and useful) CCL thomas ------------------------------------------------------------------------------ | Prof. Thomas Bally | E-mail: BALLY@CFRUNI52 | | Institute for Physical Chemistry | | | University of Fribourg | Tel: 011-41-37 826 489 | | Perolles | FAX: 011-41-37 826 488 | | CH-1700 FRIBOURG | | | Switzerland | | ------------------------------------------------------------------------------ From Patrick.Bultinck@rug.ac.be Mon Jun 27 04:03:35 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.9/930601.1506) id DAA09823; Mon, 27 Jun 1994 03:57:48 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA27525 (5.67b/IDA-1.5 for ); Mon, 27 Jun 1994 09:57:11 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA24505; Mon, 27 Jun 94 09:54:06 +0200 Date: Mon, 27 Jun 1994 09:54:06 +0200 (MET DST) From: Patrick Bultinck Subject: basis set dependency of elec. pot. To: chemistry@ccl.net In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 841 Hello netters, Maybe that after the previous quite vulgar and, in my opinion CCL-rules violating discussions we might get down to Computational Chemistry again. A question I posted earlier, but that without any doubt went amist due to the above mentionned discussion goes like this : Does anybody have a reference, or rather an opinion or experience with the basisset dependance of the electrostatic potential. I would like to fit the charges to this potential since the n-dep. in S^nPS^(1-n) in Mulliken (n=0) and Lowdin PA (n=0.5) scares me off a little. That is why I would like to know how the basis set dep. of the elect. pot. behaves compared with the MPA and LPA approaches... Any comments much appreciated, (let me know if interested in a summary) Patrick, University of Ghent, Belgium, Patrick.Bultinck@rug.ac.be From moret@far.ruu.nl Mon Jun 27 08:03:36 1994 Received: from accucx.cc.ruu.nl for moret@far.ruu.nl by www.ccl.net (8.6.9/930601.1506) id HAA10516; Mon, 27 Jun 1994 07:37:12 -0400 Received: from far.ruu.nl (ruucmc.far.ruu.nl) by accucx.cc.ruu.nl with SMTP id AA24587 (5.65c/IDA-1.4.4 for ); Mon, 27 Jun 1994 13:37:07 +0200 Message-Id: <199406271137.AA24587@accucx.cc.ruu.nl> Received: by ruucmc.far.ruu.nl (16.6/16.2) id AA03094; Mon, 27 Jun 94 13:35:17 +0200 From: "E.E.Moret" Subject: Semi-empirical S-charges II To: chemistry@ruucmc.far.ruu.nl Date: Mon, 27 Jun 94 13:35:16 METDST Name: Ed Moret Organisation: Utrecht University Phone: 030 - 536979 Mailer: Elm [revision: 66.25] Dear colleagues, With regards to the question about 'sensible' charges on sulfur atoms: The first responses to my question have arrived (thanks) and suggest to me that I need to clarify 2 things: - the CH3-SO2-NH-CH3 is only a test model for the sulfonamide containing bioactive compounds with approximately 100 atoms. Large basis set ab initio calculations could only be applied to part of the molecules. - Potential derived charges may be the best for modelling purposes and they may be less basis set dependent. Is this correct, even if the basis set lacks incorporation of d-orbitals? I calculated the ESP (Bessler, Merz, Kollman) charges with Mopac93: Molecule Ch3-SO2-nh-ch3 (important atoms in capital letters): Atom Mulliken ESP C -0.82 -0.99 S 2.53 2.45 N -0.78 -0.96 O -0.84 -0.78 O -0.91 -0.88 I will summarise the reponses for CCL. Bests regards, Ed Moret ------------------------------------------------------------------------- E.E. Moret (@more@) E.E.Moret@far.ruu.nl Computational Medicinal Chemistry/Department of Pharmaceutical Chemistry Faculty of Pharmacy/Utrecht University/the Netherlands Telephone (31-30)536979/536958 Facsimile (31-30)516674 ------------------------------------------------------------------------- From aiba@volta.vmsmail.ethz.ch Mon Jun 27 08:12:46 1994 Received: from bernina.ethz.ch for aiba@volta.vmsmail.ethz.ch by www.ccl.net (8.6.9/930601.1506) id HAA10557; Mon, 27 Jun 1994 07:49:24 -0400 Message-Id: <199406271149.HAA10557@www.ccl.net> Received: from VOLTA.vmsmail.ethz.ch by bernina.ethz.ch id <21749-0@bernina.ethz.ch>; Mon, 27 Jun 1994 13:49:01 +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: Re: "structuring CCL!" by Prof. Thomas Bally Date: Mon, 27 Jun 1994 13:49:01 +0200 Hello netters, At present, I very much like the suggestion by Prof. Thomas Bally about further structuring of CCL depending on the software in use. But I have a fear that that way CCL might lose the flexibility which it certainly possesses now. And who knows, if CCL will be further structured, then some users will benefit (?) from that but some may lose (especially those who have slow terminals with single window and therefore cannot quickly observe many lists). Another question is how costly will be the implementation of the idea of CCL further structuring for those who look after CCL. That I don't really know. So, on the second thought I am inclined to deal with the unstructured CCL even at the cost of strangely looking subject line like "CCL: G92 ..." I think we can deal with such subject line. We can just agree about certain syntax in the subject line. Consider for instance a sequence in the subject line: [1] [2] [3] [4] where [1] is GEN - for "general" questions or G92 - for Gaussian92 or any abbrevaition of any other software; or ... - some abbreviation for something else other users find useful; [2] is QUE - for question or ANS - for answer or ... - some abbreviation for something else users of CCL find useful; [3] is reserved for further specifications using KEYWORDS inherent for the software stated in position [1], e.g. CIS [4] is just sender dependent information with ultimate subject specification. Returning to the question I posted last time, the subject line obeying above rules would look like: CCL: G92 QUE CIS coeff. for exc. states It is not very bad, isn't it ? Of course, these "rules" should NOT be obligatory and must be used only by those who want to attract attention of specific audience. Thank you, -------------------------------------------------------- -------------- 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 Tim_Mitchell-1%notes@sb.com Mon Jun 27 12:03:45 1994 Received: from phinet.smithkline.com for Tim_Mitchell-1%notes@sb.com by www.ccl.net (8.6.9/930601.1506) id LAA13792; Mon, 27 Jun 1994 11:24:09 -0400 Received: by phinet.smithkline.com (5.57/ULTRIX-az-040392); id AA08329; Mon, 27 Jun 94 11:17:55 -0400 Received: by pho018.sb.com (IBM OS/2 SENDMAIL VERSION 1.2.15T (03/09/94)/1.0) id AA2198; Mon, 27 Jun 94 11:22:53 -0700 Message-Id: <9406271822.AA2198@pho018.sb.com> Received: from SB_PHARM_RD with "Lotus Notes Mail Gateway for SMTP" id 000003FECDD94B948525607B005486D1; Mon, 27 Jun 94 11:22:52 To: CHEMISTRY From: Tim Mitchell-1 Date: 27 Jun 94 16:22:40 ES Subject: CCL: Replies to assessing Langevin Dynamics calculations Mime-Version: 1.0 Content-Type: Text/Plain Very many thanks to those of you who helped with my query. The replies were as follows: From: arne @ hodgkin.mbi.ucla.edu ("'Arne Elofsson (arne@hodgkin.mbi.ucla.edu)'") @ INET I had a paper in JMB (1993:233(760-780) last year where I adressed some of the general questions. The conclusion could almost be that the best simulations are the ones that stay closest to the X-ray structures, but that might not really apply if you fix some parts of the structure. You might get some othr ideas from that paper too. arne -------------------------------------------- From: chandra @ yorvic.york.ac.uk (Chandra Verma) @ INET I remember i came up with this problem a few years ago and of course did not do much about it - but on talking to some people we gathered that perhaps an examination of the rms drift/fluctuations of the different regions would be a good starting point. you could examine the velocities (temperature) of different regions of the protein to see if it equilibrated well. -------------------------------------------- From: GKING @ arserrc.gov @ INET Hello Tim, One thing you could analyse is the statistics of the potential energy. In my molecular dynamics simulations I calculate the mean, median, and most probable potential energies. When these three values are close to one another I'm satisfied that the system is at equilibrium. There are a couple of other things you could look at such as rms fluctuations of the atoms or velocity autocorrelation functions, but these are not useful unless you have similar information from experiment or other simulations to compare with. Regards, Greg ==================================================================== Gregory King Internet: gking@arserrc.gov Eastern Reg. Res. Ctr., ARS, USDA Voice: (1) 215 233 6675 600 East Mermaid Lane Fax: (1) 215 233 6559 Philadelphia, PA 19118-2551 ==================================================================== -------------------------------------------- From: alex @ mmiris.ab.umd.edu @ INET Take a look at the potential energy with respect to time or the RMS difference with respect to the starting structure. Both act as a check to see if the system is still finding lower energy regions of conformational space or is fluctuating in a stable region. Alex MacKerell, alex@mmiris.ab.umd.edu School of Pharmacy University of Maryland at Baltimore 20 North Pine Street Baltimore, MD 21201 410-706-7442 -------------------------------------------- From: tennant%hau410.uk.sb.com @ sb.com (Mike Tennant) @ INET Hi Tim, look at the RMS deviations across the run for various subsets of atoms eg CA/ backbone/ sidechains/ solvent and make sure these are stable. This gives a better indication than energy fluctuations, esp as you are doing LD. Also look at the radius of gyration as an indicator of structural stability (this is a measure of the packing of the structure). To check that your run makes sense, you should calculate some correlation functions and compare with literature values in full solvent simulations. This will show whether the friction coefficients have been effective in reproducing solvent behaviour eg calc various ring flip and atom displacment correlation functions. I can find out some papers for comparison if you haven't got them already. cheers, Mike. -------------------------------------------- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _____ ____ _/ SmithKline Beecham Pharmaceuticals Ltd _/ _/ / ___\\\\ _ \ _/ Brockham Park _/ _/ | |___ \\|_| | _/ Tim Mitchell, Comp. Chem. Betchworth _/ _/ \___ | | _ < _/ Phone: (0)737 36 4535 Surrey _/ _/ ____| | | |_| | _/ Fax: (0)737 36 4539 RH3 7AJ _/ _/ \____/ |____/ _/ E-Mail: Tim_Mitchell-1%notes@sb.com U.K. _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From JAMES@unca.edu Mon Jun 27 15:03:48 1994 Received: from uncavx for JAMES@unca.edu by www.ccl.net (8.6.9/930601.1506) id OAA17854; Mon, 27 Jun 1994 14:48:25 -0400 Received: from uncavx.unca.edu by uncavx.unca.edu (PMDF V4.3-8 #5911) id <01HE1GQFQYOG90MVYY@uncavx.unca.edu>; Mon, 27 Jun 1994 14:48:14 EDT Date: Mon, 27 Jun 1994 14:48:14 -0400 (EDT) From: "Charles G. James" Subject: Questions about CAChe To: CHEMISTRY@ccl.net Message-id: <01HE1GQFRHZ690MVYY@uncavx.unca.edu> Organization: University of North Carolina at Asheville X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Is anyone using CAChe: a) To do undergraduate teaching 1-3 year? b) To do transition metal modeling(ZINDO)? Your opinions, problems and comments would be welcome. Charles G. James, Jr. Assoc. Professor of Chemistry Dept. of Chemistry, University of North Carolina at Asheville Asheville, NC 28804-3299, USA, Phone: (704)251-6443 FAX: (704)251-6041 E-mail: james@unca.edu From chemdcl3@emrycc.cc.emory.edu Mon Jun 27 15:06:40 1994 Received: from accucx.cc.ruu.nl for chemdcl3@emrycc.cc.emory.edu by www.ccl.net (8.6.9/930601.1506) id OAA17496; Mon, 27 Jun 1994 14:17:35 -0400 Received: from far.ruu.nl (ruucmc.far.ruu.nl) by accucx.cc.ruu.nl with SMTP id AA03538 (5.65c/IDA-1.4.4 for ); Mon, 27 Jun 1994 20:17:29 +0200 Received: from emoryu1.cc.emory.edu by ruucmc.far.ruu.nl with SMTP (16.6/16.2) id AA03333; Mon, 27 Jun 94 20:15:37 +0200 Received: from emrycc.cc.emory.edu by emoryu1.cc.emory.edu (5.65/Emory_cc.3.5.2) via