From aiba@volta.vmsmail.ethz.ch Sun Jun 26 12:03:26 1994 Received: from bernina.ethz.ch for aiba@volta.vmsmail.ethz.ch by www.ccl.net (8.6.9/930601.1506) id LAA01352; Sun, 26 Jun 1994 11:14:18 -0400 Message-Id: <199406261514.LAA01352@www.ccl.net> Received: from VOLTA.vmsmail.ethz.ch by bernina.ethz.ch id <04156-0@bernina.ethz.ch>; Sun, 26 Jun 1994 16:58:02 +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. Coefficients of determinants in CIS (exc.st.). Date: Sun, 26 Jun 1994 16:58:02 +0200 Hello netters, I run G92 and calculate excited states using CIS. In the output of such job one normally gets (apart from other things) the expansions of excited states over substituted determinants. It seems, however, that G92 gives only those coefficients which are greater than 0.1. How to override this option and to get all coefficients regardless their values ? Does anybody know ? Thanks, Ayaz Bakasov ---------------------------------------------------------------------- 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 landman@gluon.physics.wayne.edu Sun Jun 26 12:17:04 1994 Received: from CMS.CC.WAYNE.EDU for landman@gluon.physics.wayne.edu by www.ccl.net (8.6.9/930601.1506) id LAA01278; Sun, 26 Jun 1994 11:13:40 -0400 Received: from gluon.physics.wayne.edu by CMS.CC.WAYNE.EDU (IBM VM SMTP V2R2) with TCP; Sun, 26 Jun 94 09:52:51 EDT Received: by gluon.physics.wayne.edu (4.1/SMI-4.1) id AA19553; Sun, 26 Jun 94 09:52:43 EDT Date: Sun, 26 Jun 94 09:52:43 EDT From: landman@gluon.physics.wayne.edu (Joe Landman) Message-Id: <9406261352.AA19553@gluon.physics.wayne.edu> To: CHEMISTRY@ccl.net Subject: Science, Jobs, and disparaging remarks. Fellow Net.Landers: I read Mr Boehm's writing with much dismay. He has one point which is actually valid, but never supported it in his writing. THis point is relevant to all sciences at this juncture, and it should be addressed by all scientists. The point is, we have far too many new PhD's entering a shrinking science and industrial marketplace. This is the point that the YSN is trying to disseminate amoung the scientific societies. Mr Boehm failed to give this point the time it deserved, writing instead some quite inflammatory comments about who does and does not deserve a job. Back to the relevant point. Whether people in the Chemical, Physical, or engineering communities like it or not, we produce far too many people to fill available positions. We put these people into holding patterns with soft money positions, 2 post docs, research professor (non-tenure track). We must also face the fact that in the current market sceanario, this funding and position situation is unlikely to change. Rather, it is likely to get worse. This MUST be taken into account when taking on new students. Be upfront about the situation. You will find the most talented able students will remain, and the more pedestrian students will not make plans for positions that they will likely never obtain. I know this well, as I am going to finish up my PhD within the year, and the job situation is so bad, I am giving serious consideration to leaving science, and growing my fledgling computer consultancy. That is, I cannot see spending time (2-4 years) in a post-doc with no hope whatsoever of getting a tenure track position. Aside from this due to the extreme lack of science positions in industry, after a post-doc there would be no place for me to go in an established organization. Startup monies from SBIR and other places are not viable for my area, and the likelyhood of my getting any are quite small. No one owes me a job, no one is displacing me, I just have a very tough decision to make. However, there is a tough decision that the established science must make. What to do about this? YSN is trying to help by debating many possible solutions, and presenting the results of that debate to the scientific societies. It is in every scientists personal interest to aid in these discussions for the following reason. If the governments decide that physical research (aside from medical related) should not have public funding, or should be drastically reduced, how many of you would no longer have money to do experiments, hire student workers, etc? Is this a possibility? Well, it would not be politically costly for the people making the decisions, and it would free up a great deal of money for their own pet projects... Yeah... its quite possible. My point is, lets clean up our house, and fix the problems BEFORE the governments decide to fix it themselves. An old (Chinese?) story I once heard about governments solving problems goes like this. Two people go to the ruler and make their cases about why they are having problems. The ruler heaves a sigh and says "But if I kill you both then I no longer have a problem, my problem being the settlement of your problem"... Let us not put our respective sciences into such a predicament. Help fix it, by participating in discussions with YSNers about possible solutions. As I had said, this is very much related to science, Chemistry, Physics, Engineering, etc. The solution to the problem should be posed and worked on internally. (stepping off my soap box) Joe Landman landman@hal.physics.wayne.edu (new .sig under construction) ps: There are always a few people who deny that this problem exists. I urge them to get their heads out of the proverbial sand and look around. It is pervasive, and getting worse that it is now. From moret@far.ruu.nl Sun Jun 26 12:27:03 1994 Received: from accucx.cc.ruu.nl for moret@far.ruu.nl by www.ccl.net (8.6.9/930601.1506) id LAA00339; Sun, 26 Jun 1994 11:04:55 -0400 Received: from far.ruu.nl (ruucmc.far.ruu.nl) by accucx.cc.ruu.nl with SMTP id AA05139 (5.65c/IDA-1.4.4 for ); Sun, 26 Jun 1994 13:43:30 +0200 Message-Id: <199406261143.AA05139@accucx.cc.ruu.nl> Received: by ruucmc.far.ruu.nl (16.6/16.2) id AA02515; Sun, 26 Jun 94 13:41:41 +0200 From: "E.E.Moret" Subject: Semi-empirical S-charge: 'right' or 'wrong' ? To: chemistry@ruucmc.far.ruu.nl Date: Sun, 26 Jun 94 13:41:40 METDST Name: Ed Moret Organisation: Utrecht University Phone: 030 - 536979 Mailer: Elm [revision: 66.25] Dear colleagues, A good scientific discussion is appropriate and let me be the first to say that I am aware of the fact that my subject line is questionable. There is no right or wrong charge. Atomic point charges are merely a useful concept in computational chemistry. However, the semi-empirical charges I have obtained for the hypervalent S atom are a problem. They disrupt molecular mechanics calculations that I want to perform. I face the problem of accepting these charges or considering them useless for my purpose (docking). Here is my dilemma: We are currently studying molecules with around 100 atoms of which a sulfonamide group is of relevance. Apart from a geometry that does not correpond to X-ray and ab initio information, we observe large positive charges on the S atoms. Some calculation results on the molecule CH3-SO2-NH-CH3 follow. The C-S-N-C torsion angle in the input file was close to the ab initio and X-ray data of 70 or -70. I used MINDO3,MNDO,AM1,PM3 Hamiltonians in Ampac 2.1, Mopac 5, Mopac 6 and Mopac 93. The partial charge on the S atom varied between 1.6 and 2.6 ! Fortunately, there was no programme dependency, apart from programmes that explicitly mentioned the use of a different Hamiltonian for one element. This would be a typical result for the S-charge (Mopac93): sulfa_opt_MINDO3: 6 S 1.849085 sulfa_opt_MNDO: 6 S 1.632472 sulfa_opt_AM1: 6 S 2.526724 sulfa_opt_PM3: 6 S 2.159568 The input-file with cartesian coordinates is appended at the bottom. Besides interesting geometry and charge, the bond orders for the bonds from S to C or N are typically 0.7, whereas the bond orders for the bonds >from S to O are 1.15. I consider the system size prohibitive for ab initio calculations and I hesitate to use an empirical charge calculation. I would value your input on the following questions: - am I wrong in considering the current results conspicuous? - should I accept the current charges, geometry and bond orders? - should I turn to more rigorous or more empirical methods? - should I fiddle the current charges (i.e. changing the S valency by hand and substracting some pos. charge of S and some neg. charge of its neighbouring atoms, which would be a manual reduction? - are their experimental data which would allow me to check whether the current results predict the right interaction or behaviour of S-containing compounds. - will the P atom give comparable results? For those who noticed that I avoided naming P and S. Is it a phosphorus atom and a sulphurous atom or is sulphur and phospor correct english? I am looking forward to your ideas on this topic. With best 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 ------------------------------------------------------------------------- AM1 T=3600 NOINTER PRECISE BONDS ./sulfa_opt_AM1.dat 0001 0.0000 0000 0.0000 0000 0.0000 0000 0000 0000 0000 0001 1.7964 0000 0.0000 0000 0.0000 0000 0000 0000 0000 0001 1.4572 0000 3.3222 0000 0.0000 0000 0000 0000 0000 0001 3.5945 0000 3.7754 0000 0.5259 0000 0000 0000 0000 0006 0.8982 0000 0.1420 0000 0.6190 0000 0000 0000 0000 0016 0.8981 0000 1.7989 0000 1.3224 0000 0000 0000 0000 0007 1.6790 0000 3.0433 0000 1.0195 0000 0000 0000 0000 0006 3.1526 0000 2.9846 0000 1.1500 0000 0000 0000 0000 0001 0.8982 0000 -0.5819 0000 1.4472 0000 0000 0000 0000 0001 3.5287 0000 2.0089 0000 0.8086 0000 0000 0000 0000 0001 3.4511 0000 3.1472 0000 2.1961 0000 0000 0000 0000 0008 0.4152 0000 1.4318 0000 2.6394 0000 0000 0000 0000 0008 -0.3714 0000 2.2528 0000 0.7887 0000 0000 0000 0000 From aiba@volta.vmsmail.ethz.ch Sun Jun 26 13:03:24 1994 Received: from bernina.ethz.ch for aiba@volta.vmsmail.ethz.ch by www.ccl.net (8.6.9/930601.1506) id MAA03725; Sun, 26 Jun 1994 12:07:50 -0400 Message-Id: <199406261607.MAA03725@www.ccl.net> Received: from VOLTA.vmsmail.ethz.ch by bernina.ethz.ch id <04612-0@bernina.ethz.ch>; Sun, 26 Jun 1994 18:07:48 +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: Self-reply: G92 -coefficients in CIS expansions Date: Sun, 26 Jun 1994 18:07:48 +0200 Dear netters, I've posted a question about how to get from G92 more coefficients in CIS excited states expansions. In the meantime, examination of the FORTRAN code for link L914.F of G92 showed that the following option must be specified in the job card: IOp(9/40=N) and G92 will give you those coefficients in the CIS expansions for excited states which are greater than 10^(-N). Specifying large enough N, one easily gets all essential (to the required accuracy) coefficients. 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?! Thank you, Ayaz Bakasov. ---------------------------------------------------------------------- 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 ----------------------------------------------------------------------