From jeremy@med.su.oz.au Thu Feb 16 01:40:04 1995 Received: from blackburn.med.su.oz.au for jeremy@med.su.oz.au by www.ccl.net (8.6.9/930601.1506) id BAA20645; Thu, 16 Feb 1995 01:17:55 -0500 Received: (jeremy@localhost) by blackburn.med.su.oz.au (8.6.8.1/8.6.4) id RAA26399 for chemistry@ccl.net Thu, 16 Feb 1995 17:17:47 +1100 From: Jeremy R Greenwood Message-Id: <199502160617.RAA26399@blackburn.med.su.oz.au> Subject: Modelling a protein under point mutation To: chemistry@ccl.net Date: Thu, 16 Feb 1995 17:17:46 +1100 (EST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1183 Greetings to all, I have just been approached with a project concerning the modelling of the changes in structure and function of a protein under various point mutations. The X-ray crystal structure is known, as are all the different inherited single point mutations which lead to a particular pathology. Not being a protein modeller by trade, I'm asking for some preliminary qualitative advice: * Roughly how hard is it to model changes in structure or binding resulting from a single point mutation? (apparantly many such typical mutations are from charged to uncharged residues). Is it feasible to obtain meaningful results, given the state of the art? (obviously this will depend on the given system, but perhaps some out there have attempted this kind of problem previously.) * What kinds of tools are necessary or useful? (e.g. AMBER, MD, MC, simulated annealing, semi-empirical calculations on local regions with substrate binding, etc.) Which software packages are recommended (anything cheaper than Biosym?) and what level of hardware? * Any other advice for the neophyte protein modeller? Recommended texts? Summary to follow, as per usual. Naively, Jeremy From CHEM8@vax.york.ac.uk Thu Feb 16 04:40:03 1995 Received: from leeman.york.ac.uk for CHEM8@vax.york.ac.uk by www.ccl.net (8.6.9/930601.1506) id DAA21633; Thu, 16 Feb 1995 03:59:03 -0500 Via: uk.ac.york.vax; Wed, 15 Feb 1995 18:31:33 +0000 Date: Wed, 15 Feb 95 18:32 GMT From: "John Waite, Tel: ++30-1-7238958, N.H.R.F., Organic Chemistry Institute, Vas. Konstantinou 48, Athens 116-35" To: CHEMISTRY Subject: wanted: a 'ghost' writer' Message-ID: <"leeman.yor.446:15.01.95.18.39.50"@york.ac.uk> Hi Netters, Does anyone out there like writing papers to be submitted to journals? If so, I'm interested in setting up a collaboration since I now consist of a group of one person, with many ideas, sufficient computer time but little real time/inclination for writing up the results. I usually reckon to have about two papers published per year, in computational chemistry, on the calculation of Non-Linear Optical properties (polarisabilities and first and second hyperpolarisabilities, i.e. alpha, beta and gamma), particularly the latter, by semi-empirical and ab initio methods. Also, associated with these computations are geometry optimisation and basis set development. I envisage such a collaboration to consist of: Me doing the computations and preparation of the tables of results, plus suggestions of the nature of the analysis of these. i.e. the general/overall theme of the paper. While the 'ghost' writer will put things together, from abstract to references. For this the accepter of this partnership will be co-author in three out of every four publications. He/she must be fluent in English and have access to a phone, FAX and e-mail. I can probably provide the final typing facility and others may be co-authors. Please include comments, suggestions, reservations, restrictions and qualifications (limitations or conditions on the collaboration) to the above proposal in your reply. Looking forward to hearing from a suitable person, Dr. John Waite From thys@inch.uia.ac.be Thu Feb 16 05:41:24 1995 Received: from inch.uia.ac.be for thys@inch.uia.ac.be by www.ccl.net (8.6.9/930601.1506) id FAA21895; Thu, 16 Feb 1995 05:15:35 -0500 Received: by inch.uia.ac.be (5.x/SMI-SVR4) id AA02029; Thu, 16 Feb 1995 11:03:54 +0100 Date: Thu, 16 Feb 1995 11:03:53 +0100 (MET) From: Gerd Thys X-Sender: thys@inch.uia.ac.be To: "John Waite, Tel: ++30-1-7238958, N.H.R.F., Organic Chemistry Institute, Vas. Konstantinou 48, Athens 116-35" Cc: CHEMISTRY Subject: Re: CCL:wanted: a 'ghost' writer' In-Reply-To: <"leeman.yor.446:15.01.95.18.39.50"@york.ac.uk> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Mr Waite, That was a rather strange message you sent! It's an interesting offer, but since I am not the boss in my group, I cannot promise you anything... But for now, I'm interested in your articles, since I want to start working on NLO too (by using semi-empirical methods) Can you please point me to your output... I hope you get a lot of response! I can imagine being some sort of Scientific Robinson Crusoe becomes rather frustrating... 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 ---------------------------------------------------------------------------- From dmit@nmr1.ioc.ac.ru Thu Feb 16 07:40:07 1995 Received: from nmr1.ioc.ac.ru for dmit@nmr1.ioc.ac.ru by www.ccl.net (8.6.9/930601.1506) id HAA22988; Thu, 16 Feb 1995 07:24:14 -0500 Received: from [193.124.3.49] by nmr1.ioc.ac.ru with SMTP (WG7Jv1.07b+CWRU/BIOCv1.93) id AA1523 ; Thu, 16 Feb 95 15:24:12 MST Date: Thu, 16 Feb 95 15:24:06 +0300 From: "Dmitry E. Dmitriev" Message-Id: <67144.dmit@nmr1.ioc.ac.ru> X-Minuet-Version: Minuet1.0_Beta_17A Reply-To: X-POPMail-Charset: IBM 8-Bit To: chemistry@ccl.net Subject: cavity size in crowns Dear Netters! I'm looking for references to algorithms or programs which are used to calculate cavity sizes in crown ethers. Also, I would like to know about molecular modelling packages, which can be estimate this parameter. Thanks in advance. Dmitry ============================================================================ Dmitry E. Dmitriev, ** E-mail: dmit@nmr1.ioc.ac.ru NMR Centre Moscow ** ***************** N.D. Zelinsky Inst. of Org. Chem., ** tel : 7 (095) 135 90 94 Russian Academy of Sciences ** fax : 7 (095) 135 53 28 ============================================================================ From TOMKINSON_NP@fisonspharm.co.uk Thu Feb 16 09:40:08 1995 Received: from bit158.fisonspharm.co.uk for TOMKINSON_NP@fisonspharm.co.uk by www.ccl.net (8.6.9/930601.1506) id JAA24936; Thu, 16 Feb 1995 09:32:32 -0500 Received: from mr.fisonspharm.co.uk by BIT158.FISONSPHARM.CO.UK (PMDF V4.3-10 #6968) id <01HN4CNKW2XC0014S6@BIT158.FISONSPHARM.CO.UK>; Thu, 16 Feb 1995 14:33:03 +0000 (GMT) Received: with PMDF-MR; Thu, 16 Feb 1995 14:29:44 GMT MR-Received: by mta IOS; Relayed; Thu, 16 Feb 1995 14:30:07 +0000 MR-Received: by mta BIT158; Relayed; Thu, 16 Feb 1995 14:32:45 +0000 Alternate-recipient: prohibited Disclose-recipients: prohibited Date: Thu, 16 Feb 1995 14:20:00 +0000 (GMT) From: Nicholas Tomkinson Subject: RE: charges schemes with CoMFA To: chemistry%ccl.net%smtp%WPC%IOS@mr.fisonspharm.co.uk Message-id: <01HN4CNNO0JQ0014S6@mr.fisonspharm.co.uk> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=ISO-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE Posting-date: Thu, 16 Feb 1995 14:24:00 +0000 (GMT) Importance: normal Priority: normal X400-MTS-identifier: [;44924161205991/334642@UKC] A1-type: MAIL Hop-count: 3 Dear all, My thanks to all who replied.=20 =20 If I were impertinent enough to summarise I would say that the cons= ensus is : ESP charges are best and there are faster routines in later version= s of software. Coulson are ok for Comfa though. And then of the semi-empirical methods for charges MNDO better than AM1 better than PM3, the standard being ab initio = 6-31G*. This is confirmed by work done by Carlos Aleman=20 in J. Comp. Chem vol 14 1993 799-808 but in which PM3 is suggested = to be=20 best for studying MEPs. I hear good things about SAM1 and MNDO/D as well because they expli= citly=20 include d-orbitals which can't be a bad thing.=20 Going on the principals of a) time equals money, b) if you don't ha= ve the best=20 then use what you have got and c) if you can't be right be consiste= nt, then I shall probably use MNDO coulson charges especially since the versio= n I have=20 now handles sulphur. Since I have been getting some really strange bent sp2 nitrogens fr= om mopac=20 optimisations and in addition a lot of=20 my compounds have amides in, then I shall probably just use molecul= ar mechanics=20 geometries and use single point charges - although comments on this= would be=20 appreciated if someone in the know thinks this is a 'bad thing'. On= the=20 question of consistency though I have to agree with Konrad Koehler = that if=20 a method introduces random errors these will just add to the noise = in the data but not as much as being inconsistent will. Nobody really commented on the use of dielectric - maybe this is be= cause all the methods are as bad as each other in modelling water and that vacuum= =20 conformations are about as much use as a woolly raincoat. I shall c= hoose a=20 dielectric that reproduces what little experimental evidence I have= and use that=20 consistently throughout the series of molecules. These calculations= are in my=20 opinion not worth the time and effort required for a rigorous treat= ment. =20 =20 > #################################################################= ########## > I have two statements and a question for you. >=20 > 1) My experience of fitting charges using CHELPG to ab initio res= ults > indicates that the charges you get vary somewhat due to conformat= ion > (10-20%). As I'm using MD I just use an "average charge". =20 >=20 > 2) As I'm sure many others will tell you Mulliken charges bear li= ttle > resemblance to the charges produced by any of the ESP fit methods= . This can > have a pretty significant effect on your calculation. I looked a= t MNDO, > AM1, PM3 and ab initio (up to 6-31G*). Basicly, MNDO Mulliken an= alyses are > closest to the ESP fits of the ab initio calcs. AM1 produces lar= ger charges > and PM3 larger charges still. PM3 charges were about 60% greater= than MNDO > ones in some cases. It may be slow and painful, but the only way= to quality > results is an ESP fit (to MNDO results should be fine). You migh= t be able > to save yourself some time by reducing the mesh of points where y= ou are > doing the fitting to cover those parts of the molecule that are o= f real > interest or where there is significant charge seperation. >=20 > 3) Where did you get your ESP fitter for MNDO or can I get a copy= of it. I > only have one thats part fo an ab initio package and I would love= to have > one that I could use with my semi-empirical package. >=20 > P.S. In defense of MNDO. I started out using the other two me= thods (AM1 > and PM3) and found that they didn't do nearly as good a job at ev= aluating > the energy of conformers. There are several articles in J. Comp.= Chem. > which compare the methods and indicate that MNDO did the best job= . PM3 > seriously overestimates the attraction between methyl groups. AM= 1 does > better but is still too attractive. MNDO is a little too repulsi= ve but is > still the closest fit to ab initio results. >=20 > Dr. Ross Underhill > Royal Military College of Canada > Kingston, Ontario > (613) 541-6000 X6175 >=20 > #################################################################= ########## >=20 > Nicholas >=20 > I am often concerned with validity of partial atomic charges. Th= e method=20 > I've settled on for small molecules involves full geometry optimi= zation=20 > using AM1 (the later versions handle sulfur), then resubmitting f= or an=20 > ESP-MNDO calculation with no geometry optimization (there's a hic= cup with=20 > this in that my version of sybyl generates a .dat file specifying= full=20 > geometry optimization regardless of what one wants, so I submit t= he MNDO=20 > ESP file on "hold for later" without specifying "user other MOPAC= " [this=20 > generates the proper .dat file], then outside sybyl do a "RunMopa= c etc").=20 > My concern about using MNDO for the geometry optimization as wel= l is=20 > related to inaccuracies in the charge calculations which I though= t could=20 > arise in systems with partial double bonds which MNDO might not r= ecognize=20 > too well, giving "twisted" groups which should be planar (and und= ergoing=20 > resonance). >=20 > The slowness of ESP is a problem but I believe recently is has be= en sped=20 > up considerably. I would put more trust in charges derived from = this=20 > than from PM3 Mulliken, although I too have also read that consis= tent use=20 > of a certain method, rather than the method itself, may be more i= mportant=20 > for CoMFA/Docking etc. >=20 > CoMFA is potentially a great method, although I would like to see= the=20 > ability to incorporate hydrophobic fields (which can be done by= =20 > interfacing to HINT, by G. Kellogg) and flexible molecules should= be used=20 > with caution. > =20 > People have suggested various dielectric constants for emulating = a=20 > protein interior (which is I suppose what you are after), varying= from 4=20 > to something in the 30s, as an alternative to a distance-dependan= t=20 > dielectric, but I am unaware of one being a "clear winner". >=20 > As a chemist with little time recently for modelling, I would lik= e to=20 > validate the above, which are essentially "hunches"; please can I= see=20 > your answers if you don't post them to the net. >=20 > +----------------------------------------------------------------= ------+ > Dr Jonathan Ball > CSIRO, Division of Animal Health = =20 > Private Bag 1, Parkville, Victoria 3052, Austra= lia=20 > Internet email: baell@mel.dah.csiro.au = =20 > Tel: +61 3 342-9782 Fax: +61 3 347-4042 = =20 > +________________________________________________________________= ______+ >=20 >=20 > #################################################################= ########## >=20 > Dear Dr. Tomkinson, >=20 > I read with interest your comments about semiempirical charges = for > CoMFA work. I have a few comments that may be helpful in the con= text=20 > of your questions: >=20 > - PM3 is known to be unreliable for charges. The reasons for th= is > are relatively well-known, but I would certainly NOT depend on= these > charges for analyses such as you are carrying out. While cert= ainly > not perfect, I think that AM1 is usually considered to be more > reliable than PM3 for quantities related to analysis of the mo= le- > cule's wavefunction. AM1 can be found in many places, especia= lly > the various versions of AMPAC amd MOPAC now available. The AM= 1 > reference is: Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.;= =20 > Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902. >=20 > - I would NEVER recommend using Mulliken-derived charges with a = mini- > mal basis set semiempirical method like AM1 or PM3. The basis= set > dependency of Mulliken makes the application of this method= =20 > essentailly invalid. I hope that when you WROTE "Mulliken" yo= u > MEANT "Coulson". This is the technique that is used by defaul= t > in both AMPAC and MOPAC and these charges are those that are > reported in the OUT and ARC files resulting from these program= s. > References to the Coulson approach are: 1) Armstrong, D. R.; P= erkins > P. G.; Stewart, J. J. P. J. Chem. Soc., Dalton 1973, 838; = =20 > 2) Pople, J. A.; Beveridge, D. L. Approximate Molecular Orbita= l=20 > Theory; McGraw-Hill: New York, 1970; pp 67. >=20 > - Both MNDO and AM1 have sulfur parameters in modern implemen- > tations of the methods. >=20 > - ESP is a good charge method and may run much faster in some pr= ograms > than others. You should look around. >=20 > Cheers, Andy Holder >=20 > =3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-= =3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-= =3D-=3D-=3D-=3D-=3D > DR. ANDREW HOLDER > Assistant Professor of Computational/Organic Chemistry >=20 > Department of Chemistry || Internet Addr: aholder@cctr.= umkc.edu > Univ. of Missouri - Kansas City || Phone Number: (816) 235-229= 3 > Spencer Chemistry, Room 315 || FAX Number: (816) 235-550= 2 > Kansas City, Missouri 64110 || > =3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-= =3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-= =3D-=3D-=3D-=3D-=3D >=20 > #################################################################= ########## >=20 > Hi Nicholas, >=20 > Partial charges can be calculated from wave functions (semiemp or= ab initio) > by the Mulliken or ESP, among other methods. The ESP method is be= tter > because is less basis set dependent and reproduces dipole moments= much > better than Mulliken charges. So I would recommend the use of ESP= . > I'm using AM1 and ab initio 321G* results and they show the same = trends in=20 > dipoles calculated from ESP charges (it doesn't happen with Mulli= ken). > The trends are for many conformations of 20 - 50 atoms molecules. > Now, if you need something faster that also reproduces dipoles yo= u > can use Charge Equilibration method from Rappe & Goddard, J.Phys.= Chem., > 95,3358-3363,1991. It's realy fast and you don't even need a wave= func. >=20 > Edgardo Garcia > Univ. of Colorado > BOULDER CO USA >=20 > #################################################################= ########## >=20 > Subject: Re: CCL:charges schemes with CoMFA >=20 > You might want to read the material on charge fitting > under http://www.amber.ucsf.edu/amber/amber.html - > also there are pages on charges and semiempirical > charges under the 'material from the net' heading. >=20 > Bill Ross >=20 > #################################################################= ########## >=20 > Subject: Re: CCL:charges schemes with CoMFA >=20 > See J. Med. Chem. 1993, 36, 2390. >=20 > I that paper, I performed a CoMFA on ACE inhibitors using PM3 cha= rges. >=20 > The original manuscript in that series used the same alignment ru= le > but Gast_Marsili charges. I did find that PM3 charges worked some= what > better. >=20 > In the HIV model that we published in JMC last year, we used AM1 = charges. > Not included in that paper is the model based on Gast_Huck charge= s=20 > which was comparable. >=20 > ESP charges seem to be vogue right now. In essence, I don't think > it really makes all that much difference as long as you are comfo= rtable > with the charge set (i.e. it gives reasonable looking charge dist= ributions) > and you are consistent in your treatment. >=20 > CW >=20 > *****************************************************************= *** > *Chris L. Waller, Ph.D. PHONE 919-541-79= 76* > *Research Chemist FAX 919-541-53= 94* > *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 constitu= te* > *endorsement by the United States Environmental Protection Agency= . * > *****************************************************************= *** >=20 > #################################################################= ########## >=20 >=20 > Subject: Re: CCL:charges schemes with CoMFA >=20 > You missed our papers!! Although we didn't compare AM1 with PM3 = in this > application, we see very strange charges with PM3 on nitrogens. = AM1 > gives good CoMFA models that fit & cross-validate pKa's. =20 >=20 > Pertinent references: >=20 >=20 > K. H. Kim, Y. C. Martin, Chapter in "QSAR: Rational Appraoches o= n the Design > of Bioactive Compounds", C. Silipo and A. Vittoria, Eds., Elsevi= er, > Amsterdam.", 1991 "Evaluation of Electrostatic and Steric Descr= iptors for > 3D-QSAR: The H+ and CH3 Probes Using Comparative Molecular Field= Analysis > (CoMFA) and the Modified Partial Least Squares Method" pp 151-15= 4. >=20 > Ki. H. Kim and Yvonne C. Martin, J. Org. Chem., 56, 2723-2729, 19= 91, =D2Direct > Prediction of Linear Free Energy Substituent Effects from 3D Str= uctures Using > Comparative Molecular Field Analysis. 1. Electronic Effects of S= ubstituted > Benzoic Acids=D3.=20 >=20 >=20 > K. H. Kim and Y. C. Martin, J. Med. Chem., 34, 2056-2060, 1991 = =D2Direct > Prediction of Dissociation Constants (pKa=D5s) of Clonidine-like= Imidazolines, > 2-Substituted Imidazoles, and 1-Methyl-2-substituted-imidazoles = =66rom 3D > Structures Using a Comparative Molecular Field Analysis )CoMFA) = Approach=D3. >=20 > In unpublished work, we also found that AM1 is just fine for phen= ols and anilines, provided that one uses the unprotonated form for th= e structure optimization. >=20 >=20 >=20 > @@@@@@@@@@@ Yvonne Martin, Senior Project Leader > @ Computer Assisted Molecular Design Project > @@@@@@@@ @ D-47E, AP10 2fl > @ @ Abbott Laboratories > @ @ 100 Abbott Park Road > @@@@@@@@@@ Abbott Park, IL 60064-3500 > Phone: 708 937-5362 FAX: 708 937-2625 >=20 >=20 > PS. The JOC article has the most comparisons. >=20 > #################################################################= ########## >=20 > Nick: >=20 > My preference for CoMFA are ab initio 6-31G* ESP fitted charg= es.[1,2] If > you only optimize bond lengths and valence angles and hold torsio= ns fixed, > these calculations are not as time consuming as you might think.= =20 >=20 > If you wish to use semiempirical methods, check out the PMEP = option [3,4] > in the most recent version of MOPAC93. It is at least 2 orders o= f magnitude=20 > faster than the Besler et al. method and more accurate. The meth= od is=20 > currently parameterized for C,H,N,O,F, and Cl. The author (wang@= irbm.it) > is currently working on parameters for S and P. >=20 > I suspect that the charges are more important than what diele= ctric > constant you use. For a more radical approach, you might check o= ut a recent > paper by Klebe et al.[5].=20 >=20 > I hope you find these references useful. >=20 > Ciao, >=20 > Konrad >=20 > ----------------------------------------------------------------= -- > | Konrad Koehler | Computational Chemistry Group = | > | internet: koehler@irbm.it | Department of Medicinal Chemistr= y | > | | IRBM = | > | telephone: +39-6-910-93606 | Via Pontina Km. 30,600 = | > | fax: +39-6-910-93225 | 00040 Pomezia (Roma) = | > | | Italy = | > ----------------------------------------------------------------= -- >=20 > (1) Allen, M. S.; La Loggia, A. J.; Dorn, L. J.; Martin, M. J.; C= ostantino, > G.; Hagen, T. J.; Koehler, K. F.; Skolnick, P.; Cook, J. M. P= redictive > binding of b-carboline inverse agonists and antagonists via t= he > CoMFA/GOLPE approach. J. Med. Chem. 1992, 35, 4001-4010.= =20 > (2) Wong, G.; Koehler, K. F.; Skolnick, P.; Gu, Z.-Q.; Ananthan, = S.; > Schonholzer, P.; Hunkeler, W.; Zhang, W.; Cook, J. M. Synthet= ic and > Computer Assisted Analysis of the Structural Requirements for= Selective, > High Affinity Ligand Binding to 'Diazepam-Insensitive' Benzod= iazepine > Receptors. J. Med. Chem. 1993, 36, 1820-30.=20 > (3) Ford, G. P.; Wang, B. A new approach to the rapid semiempiric= al calculation > of molecular electrostatic potential based on the AM1 wave fu= nction:=20 > Comparison with ab initio HF/6-31G* results. J. Comput. Chem= . 1993, 14, > 1101-1111.=20 > (4) Wang, B.; Ford, G. P. Atomic charges derived from a fast and = accurate > method for electrostatic potentials based on modified AM1 cal= culations. J. > Comput. Chem. 1994, 15, 200-207.=20 > (5) Klebe, G.; Abraham, U.; Mietzner, T. Molecular similarity ind= ices in a > comparqative analysis (CoMSIA) of drug molecules to correlate= and predict > their biological activity. J. Med. Chem. 1994, 37, 4130-41= 46.=20 >=20 > #################################################################= ########## >=20 > Nicholas: >=20 > There have been publications confirming that CoMFA models are cha= rge-scheme > insensitive; see Kubinyi, "3D QSAR in Drug Design", ESCOM, Leiden= , 1993, for > review articles summarizing the CoMFA technique. In my hands, > Gasteiger-Huckel assignment of charges appears to give CoMFA mode= ls that are > much the same as those using charges from semiempirical calculati= ons. >=20 > Phil Cruickshank >=20 > *********************************************************= **** > * Philip A. Cruickshank = * > * FMC Corporation, Agricultural Chemical Group = * > * Chemical Sciences Team = * > * P. O. Box 8, Princeton, NJ 08543 = * > * = * > * Telephone: (609)951-3646 Fax: (609)951-383= 5 * > * e-mail: pacruickshank@fmc.com = * > *********************************************************= **** >=20 > #################################################################= ########## >=20 > Hi Nick, > Hope things are fine at Loughborough. If you want a semi-emp meth= od > for charge calculations then the SAM1 method has had some good pu= blicity=20 > lately, it handles phosphrous and sulphur better than AM1. Try ta= lking to > Andy Holder (aholder@vax1.umkc.edu), you may want to get hold of = AMPAC 5.0 > for this, which if your quick you can get a 30 day trial copy... >=20 > TTFN Andy > -- > #################################################################= ############# > Structural and Computation Chemistry Group________chp1aa@uk.ac.su= rrey - JANET. > Department of Chemistry___________________________phone_______+44= -1483-259591. > University of Surrey______________________________fax_________+44= -1483-300803. > Guildford,________________________________________ftp___________1= 31.227.110.69 > Surrey, GU2 5XH, UK_________________WWW http://www.chem.surrey.a= c.uk/~chp1aa/ > #################################################################= ############# >=20 > #################################################################= ########## >=20 > Subject: Re: charges schemes with CoMFA >=20 >=20 > I will not discuss the impact of choosing partial charges in conf= ormational > analysis (CA), for two reasons: their magnitude (and "correctness= ") will > influence the choice of your local minima [to the extent that emp= irical=20 > charges may give a different energy map than quantum-mechanical o= nes], > and the choice of the dielectric D will definitely contribute to = that > [smaller D will result in higher probability of intra-molecular H= -bonds]. > MNDO ESP calculations may be slow in MOPAC, but they correlate we= ll with > 631G* ESP charges - 0.94-0.96 R^2 for charge to charge correlatio= n - > better than STO-3G ESP for the same molecules [these with G92]. > PM3 has been previously reported to go wrong with Nitrogens - it = was > previously posted on CCL - so browse in the 93-94 archive and loo= k for > messages from Drs JJP Stewart, A Holder, E Zoebisch [and others..= .]. >=20 > In CoMFA, the choice of charges does not matter as long as you ar= e consistent > throughout the series: "If you can't be right, be consistent" (Da= vid Patterson). > In my experience, MNDO vs MNDO ESP charges have no significant im= pact on > the sets I studied. Of course, there might be some tricky ones ou= t there 8=3D) > but for systems where no fancy electronic distribution occurs, MN= DO or AM1 > can do the works. Chris Waller has noted that PM3 gives better co= rrelations > than Gasteiger-Huckel, but I would point out that both models wer= e correlating > well in CoMFA. A paper I reviewed (I believe it is out in JMC) re= ported on the > side that comparing AM1 vs Gasteiger-Marsili, they found no diffe= rence. > In sum, as long as your CA results are ok, your CoMFA model is un= likely > to yield significant differences by using different partial charg= es. > As for the dielectric in CoMFA - I recently started using constan= t D instead > of distance dependent one - again, it is unlikely to have a treme= ndous > impact on the robustness/predictive/explanatory qualities of your= model. >=20 > --Tudor >=20 > *****************************************************************= *********** > * Tudor I. Oprea, MD PhDTel: (505) 667 2682 * > * Postdoctoral Research AssociateFax: (505) 665 3493 * > * Theoretical Biology and Biophysics (T-10)Email: * > * Los Alamos National Laboratorytudor@t10.lanl.gov * > * Mail Stop K710, Los Alamos NM 87545 * > *****************************************************************= *********** >=20 > #################################################################= ########## >=20 > Subject: CCL:CoMFA: charge schemes >=20 > On 10-FEB-1995, Tudor Oprea wrote in response to Nick Tomkinso= n's post: >=20 > > MNDO ESP calculations may be slow in MOPAC, but they correlate = well with > > 631G* ESP charges - 0.94-0.96 R^2 for charge to charge correlat= ion - > > better than STO-3G ESP for the same molecules [these with G92]. >=20 > The latest version of MOPAC93 includes a new option, PMEP[1,2]= which is at > least two orders of magnitude faster and more accurate (at reprod= ucing 6-31G* > ESPFIT charges) than the old MOPAC ESP charges.=20 >=20 > [1] Ford, G. P.; Wang, B. A new approach to the rapid semiempiric= al calculation > of molecular electrostatic potential based on the AM1 wave fu= nction: > Comparison with ab initio HF/6-31G* results. J. Comput. Chem= . 1993, 14, > 1101-1111. > [2] Wang, B.; Ford, G. P. Atomic charges derived from a fast and = accurate > method for electrostatic potentials based on modified AM1 cal= culations. J. > Comput. Chem. 1994, 15, 200-207. >=20 > > In CoMFA, the choice of charges does not matter as long as you = are consistent > > throughout the series: "If you can't be right, be consistent" (= David Patterson). > > In my experience, MNDO vs MNDO ESP charges have no significant = impact on > > the sets I studied. Of course, there might be some tricky ones = out there 8=3D) > > but for systems where no fancy electronic distribution occurs, = MNDO or AM1 > > can do the works. ... [rest of message deleted] >=20 > The source of charges may not matter for systems like steroids= or peptides, > where most commonly used methods (including Gasteiger-Marsili) gi= ve reasonable > charges. But in my experience, the source of charges does make a= _big_ > difference for systems such as aromatic heterocycles. We did a c= omparison of > ESPFIT 6-31G* [3] vs. MNDO Mulliken charges [3] vs. Gasteiger-Mar= sili > [unpublished]. The cross validated R2's were 0.71 vs. 0.65 vs. ~= 0.40 > respectively. >=20 > [3] Allen, M. S.; La Loggia, A. J.; Dorn, L. J.; Martin, M. J.; C= ostantino, > G.; Hagen, T. J.; Koehler, K. F.; Skolnick, P.; Cook, J. M. P= redictive > binding of b-carboline inverse agonists and antagonists via t= he > CoMFA/GOLPE approach. J. Med. Chem. 1992, 35, 4001-4010. >=20 > The use of consistent charges will of course cancel systemati= c errors in > the charges. However, if the errors are random and if the electr= ostatics > (relative to sterics, hydrophobicity, etc.) are an important part= of the > correlation, then bad charges will produce bad correlations.=20 >=20 > Ciao, >=20 > ----------------------------------------------------------------= -- > | Konrad Koehler | Computational Chemistry Group = | > | internet: koehler@irbm.it | Department of Medicinal Chemistr= y | > | | IRBM = | > | telephone: +39-6-910-93606 | Via Pontina Km. 30,600 = | > | fax: +39-6-910-93225 | 00040 Pomezia (Roma) = | > | | Italy = | > ----------------------------------------------------------------= -- >=20 > #################################################################= ########## >=20 > Subject: Re: CoMFA charges >=20 >=20 > Hi - >=20 > In regards to your question on charges. We have developed a meth= od for > obtaining partial charges that we call Charge Model 1 (CM1). The= method > is an empirical mapping of the Mulliken charges obtained by eithe= r AM1 > or PM3. Of course, everyone has their favorite method for comput= ing > partial charges and there is no way to compare directly to experi= mental > measurements. When developing CM1, we chose our method so that t= he > dipole moment calculated from our partial charges reproduced the > experimental dipole moment for that molecule as closely as possib= le. > Calculating CM1 charges takes essentially no more time than the P= M3 > calculations that you are already running but they are much more > accurate. We have incorporated CM1 into our program AMSOL which = is > available from QCPE. The paper describing our method is currentl= y in > press in the Journal of Computer-Aided Molecular Design (I unfort= unately > don't have a release date to give you). We find that, in general= , when > compared to experiment, dipole moments calculated with CM1 yield = about the > same accuracy as dipole moments calculated from HF/6-31G* CHELPG = charges, > or even the MP2/6-31G* density derived dipole moments. CM1 has b= een > developed for H, C, N, O, F, Si, S, Cl, Br, and I. I'd be happy = to send > you more information if you'd like. >=20 > David J. Giesen > giesen@chemsun.chem.umn.edu >=20 > #################################################################= ########## From jkong@is.dal.ca Wed Feb 15 14:48:19 1995 Received: from is.dal.ca for jkong@is.dal.ca by www.ccl.net (8.6.9/930601.1506) id OAA11372; Wed, 15 Feb 1995 14:48:17 -0500 Received: by is.dal.ca (AIX 3.2/UCB 5.64/4.03) id AA93527; Wed, 15 Feb 1995 15:47:48 -0400 Date: Wed, 15 Feb 1995 15:47:48 -0400 (AST) From: Jing Kong Subject: ACES2 question To: CCL Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Dear netters, For some reason, I can't get CCSD run with ACES2. Here is the error message: Could not load program xvprops Symbol #NREAD in bsh is undefined Error was: Exec format error Would you please help me out? Thanks! Regards, Jing From dimitris@3dp.com Wed Feb 15 15:29:55 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.9/930601.1506) id PAA12228; Wed, 15 Feb 1995 15:29:52 -0500 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA06268; Wed, 15 Feb 95 16:05:50 -0500 Received: by europa.3dp.com (931110.SGI) id AA06325; Wed, 15 Feb 95 16:17:43 -0500 From: "Dimitris Agrafiotis" Message-Id: <9502151617.ZM6323@europa.3dp.com> Date: Wed, 15 Feb 1995 16:17:43 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Need software to 'beautify' 2D chemical graphs Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Status: RO Are there any software packages that can take as input a connection table and produce a 'regular' (i.e. aesthetically pleasing) 2D chemical graph which can be EXPORTED to third party applications via a standard 2D coordinate file? The term 'regular' refers to graphs with standard bond lengths and angles, ring geometries etc. In other words, I am looking for algorithms that produce a publication-quality 2D representation of a molecule which is consistent with standard chemical drawing conventions. A few comments on the degree of sophistication of those programs would also be useful. I know from my LHASA days that this is NOT a trivial problem, particularly if you are dealing with complex fused/bridged systems. Thanks for your help. -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (215) 222-8950 3700 Market Street | fax: (215) 222-8960 Philadelphia, PA 19104 From JSMCM@jazz.ucc.uno.edu Wed Feb 15 15:11:01 1995 Received: from jazz.ucc.uno.edu for JSMCM@jazz.ucc.uno.edu by www.ccl.net (8.6.9/930601.1506) id PAA11906; Wed, 15 Feb 1995 15:11:00 -0500 Received: from jazz.ucc.uno.edu by jazz.ucc.uno.edu (PMDF #2820 ) id <01HN2XFXA3GW8ZSKBQ@jazz.ucc.uno.edu>; Wed, 15 Feb 1995 14:10:28 CST Date: 15 Feb 1995 14:10:28 -0600 (CST) From: JORGE Subject: Burning Surface To: CHEMISTRY@ccl.net Message-id: <01HN2XFXA3GY8ZSKBQ@jazz.ucc.uno.edu> X-VMS-To: IN%"CHEMISTRY@ccl.net" X-VMS-Cc: JSMCM MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Status: RO Dear CCL's readers: I have an urgent need to get information related to the modeling of a burning surface. One possible interest is how to model the creation of gases from the reacting surface, based on the fuel and oxidizers embedded in the surface. There is an interesting article on the recent JPC (page 1384) where it refers very shortly to several models and descriptions by Summerfield et al. Beckstead, Deer, and Price Ben-Reuven et al. Cohen et al. Ermolin et al. Hatch Williams et al. CHEMKIN-based model of Melius Merzhanov Strunin and Manelis Li et al, and Huang et al. If you have information on practical computational models or codes based on the above or any other please contact me. If this is not clear, I can give you additional information since I am making this request the shortest possible. I would appreciate any pointer or hint on the subject and I will be glad to exchange ideas on the subject. I will prepare a summary if interest arise. With best regards Dr. Jorge M. Seminario Department of Chemistry University of New Orleans New Orleans, LA70148 Phone 504-286-7216 Fax 504-286-6860 email jsmcm@uno.edu From desmarai@ERE.UMontreal.CA Wed Feb 15 15:57:42 1995 Received: from condor.CC.UMontreal.CA for desmarai@ERE.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id PAA13092; Wed, 15 Feb 1995 15:57:37 -0500 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA29058 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Wed, 15 Feb 1995 15:55:36 -0500 Received: from tornade.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA06983; Wed, 15 Feb 95 15:55:35 -0500 Received: by tornade.ERE.UMontreal.CA (940406.SGI/5.17) id AA22058; Wed, 15 Feb 95 15:55:33 -0500 From: desmarai@ERE.UMontreal.CA (Desmarais Normand) Message-Id: <9502152055.AA22058@tornade.ERE.UMontreal.CA> Subject: Q: CI and exchange integrals? To: CHEMISTRY@ccl.net (Comp.Chem.List Group) Date: Wed, 15 Feb 1995 15:55:31 -0500 (EST) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 835 Status: RO Hello, I'm looking for some conceptual discussions on the exchange integral at the CI level or any talk on the bielectronic CI correlation contributions. Any references or ideas? Furthermore: were could I find explicit formulas for the first and second order CI reduced density matrix over the AOs? - VERY IMPORTANT! ...and maybe an efficient algoritm, - COULD BE IMPORTANT! and (why not) code in Fortran or C or even C++. - WHY NOT? Please send your reply to me directly, I will sumarize for the list. Thank you for your time and attention! Normand D. -- o-----------------------------------o [ Normand Desmarais ] [ desmarai@tornade.ere.umontreal.ca ] [ desmarai@chims1.chimcn.umontreal.ca ] o-----------------------------------o From lwalsh@aries.scs.uiuc.edu Wed Feb 15 17:01:27 1995 Received: from argus.cso.uiuc.edu for lwalsh@aries.scs.uiuc.edu by www.ccl.net (8.6.9/930601.1506) id RAA14817; Wed, 15 Feb 1995 17:01:26 -0500 Received: from aries.scs.uiuc.edu (aries.scs.uiuc.edu [128.174.90.55]) by argus.cso.uiuc.edu (8.6.9/8.6.9) with SMTP id QAA52900 for <@argus.cso.uiuc.edu:chemistry@ccl.net>; Wed, 15 Feb 1995 16:01:18 -0600 Received: by aries.scs.uiuc.edu (931110.SGI/930416.SGI) for @argus.cso.uiuc.edu:chemistry@ccl.net id AA19646; Wed, 15 Feb 95 16:01:17 -0600 Date: Wed, 15 Feb 1995 16:01:17 -0600 (CST) From: Laura Walsh Subject: FLEXlm To: Computational Chemistry List Server Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO We use the MSI packages Quanta/CHARMm and Cerius2, which are managed by the license manager program FLEXlm. I would like to know if anyone has written a script to analyze the license log for statistics, such as maximum number of users, usages of each package, and/or accounting information for computers and users. It shouldn't be too hard to write, but I sure would like to avoid doing so if it is already available somewhere. Thanks. Laura Laura Lynn Walsh, School of Chemical Sciences Computer Center, Box 66-1, 152 Noyes Lab, 505 South Mathews Ave., University of Illinois, Urbana, IL 61801-3364 lwalsh@aries.scs.uiuc.edu (217) 244-0560 From steller@structchem.uni-essen.de Thu Feb 16 11:40:32 1995 Received: from gaby.structchem.uni-essen.de for steller@structchem.uni-essen.de by www.ccl.net (8.6.9/930601.1506) id KAA26743; Thu, 16 Feb 1995 10:45:17 -0500 Received: by gaby.structchem.uni-essen.de (911016.SGI/910805.SGI) for chemistry@ccl.net id AA01073; Thu, 16 Feb 95 16:44:58 +0100 From: steller@structchem.uni-essen.de (Ingo Steller) Message-Id: <9502161544.AA01073@gaby.structchem.uni-essen.de> Subject: pks/pkb - values from MO-calculations? To: chemistry@ccl.net Date: Thu, 16 Feb 1995 16:44:57 +0100 (MET) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 617 Dear Netter's, can someone give my any reference on the calculation of pks/pkb values (acid and basestrength) from MO data? What is the best way to retrieve such values and is it possible to use semiemperical methods too, escecially on radical organic bases? Sincerely, Ingo Steller. -- Ingo Steller e-mail: steller@structchem.uni-essen.de Universitaet-Gesamthochschule Essen Fachbereich 08 - Chemie Tel.: ++49 (0)201 183 3599 Institut fuer Anorganische Chemie Fax : ++49 (0)201 183 2535 Abteilung Roentgenstrukturanalyse Universitaetsstrasse 3-5 45117 Essen From herbert.homeier@rchs1.chemie.uni-regensburg.de Thu Feb 16 11:49:49 1995 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.9/930601.1506) id LAA27915; Thu, 16 Feb 1995 11:36:52 -0500 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA00765 (5.65c/IDA-1.4.4 for ); Thu, 16 Feb 1995 17:36:43 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA06195; Thu, 16 Feb 95 17:38:16 +0100 Date: Thu, 16 Feb 95 17:38:16 +0100 From: Herbert Homeier (t4720) Message-Id: <9502161638.AA06195@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: J. Math. Chem. Dear CCLers, I saw some reference to the "J. Math. Chem." in one of the postings to CCL. Since this journal is not available here, could someone please send me some information who is the publisher/editor, and how to contact him? Best regards Herbert Homeier -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: na.hhomeier@na-net.ornl.gov HOMEPAGE --------------------------------------------------------------- From jkl@ccl.net Thu Feb 16 11:53:51 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id LAA27571; Thu, 16 Feb 1995 11:22:21 -0500 Date: Thu, 16 Feb 1995 11:22:21 -0500 From: Jan Labanowski Message-Id: <199502161622.LAA27571@www.ccl.net> To: chemistry@ccl.net Subject: Sorry for empty messages Cc: jkl@ccl.net Dear Netters, Sorry for repated empty messages (you should have gotten 5 of them). If you got less then that I will resend you the missing ones {:-)}. Sorry again... My "improvement" did not work the first time. Now, since I am still trying you may get more junk mail... Sorry again, but I cannot say it will never happen again. Jan Labanowski Your friendly junk provider jkl@ccl.net P.S. Have you written your letter of support for CCL? Have you sent it or FAXed it to me? I will soon thank all of you who did... From dsg@hartree.quantchem.kuleuven.ac.be Thu Feb 16 12:40:28 1995 Received: from hartree.quantchem.kuleuven.ac.b for dsg@hartree.quantchem.kuleuven.ac.be by www.ccl.net (8.6.9/930601.1506) id MAA29393; Thu, 16 Feb 1995 12:36:15 -0500 From: Received: by hartree.quantchem.kuleuven.ac.be id AA24475 (5.67a/IDA-1.5 for chemistry@ccl.net); Thu, 16 Feb 1995 18:31:07 +0100 Date: Thu, 16 Feb 1995 18:31:07 +0100 Message-Id: <199502161731.AA24475@hartree.quantchem.kuleuven.ac.be> To: chemistry@ccl.net, steller@structchem.uni-essen.de Subject: Re: CCL:pks/pkb - values from MO-calculations? Could please send me replies of you question regarding pK calculation from MO data? Debasis Sengupta dsg@hartree.quantchem.kuleuven.ac.be From TOMKINSON_NP@fisonspharm.co.uk Thu Feb 16 13:40:34 1995 Received: from bit158.fisonspharm.co.uk for TOMKINSON_NP@fisonspharm.co.uk by www.ccl.net (8.6.9/930601.1506) id MAA29792; Thu, 16 Feb 1995 12:45:06 -0500 Received: from mr.fisonspharm.co.uk by BIT158.FISONSPHARM.CO.UK (PMDF V4.3-10 #6968) id <01HN4JCRLCA80014NB@BIT158.FISONSPHARM.CO.UK>; Thu, 16 Feb 1995 17:45:09 +0000 (GMT) Received: with PMDF-MR; Thu, 16 Feb 1995 17:41:56 GMT MR-Received: by mta IOS; Relayed; Thu, 16 Feb 1995 17:42:08 +0000 MR-Received: by mta BIT158; Relayed; Thu, 16 Feb 1995 17:44:46 +0000 Alternate-recipient: prohibited Disclose-recipients: prohibited Date: Thu, 16 Feb 1995 17:31:00 +0000 (GMT) From: Nicholas Tomkinson Subject: charges again To: chemistry%ccl.net%smtp%WPC%IOS@mr.fisonspharm.co.uk Message-id: <01HN4JCVE8WM0014NB@mr.fisonspharm.co.uk> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Posting-date: Thu, 16 Feb 1995 17:34:00 +0000 (GMT) Importance: normal Priority: normal X400-MTS-identifier: [;65147161205991/334947@UKC] A1-type: MAIL Hop-count: 3 My apologies for the control characters in my mail message. I think the problem lies with editing the file on the SG but having to mail the thing on the vax. I shall try and send it again. sigh Nick From herbert.homeier@rchs1.chemie.uni-regensburg.de Thu Feb 16 15:40:23 1995 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.9/930601.1506) id PAA03479; Thu, 16 Feb 1995 15:38:31 -0500 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA06113 (5.65c/IDA-1.4.4 for ); Thu, 16 Feb 1995 21:38:20 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA06612; Thu, 16 Feb 95 21:39:53 +0100 Date: Thu, 16 Feb 95 21:39:53 +0100 From: Herbert Homeier (t4720) Message-Id: <9502162039.AA06612@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: Summary: J. Math. Chem: Dear CCLers, Many thanks to all who replied to my question. My post was: > I saw some reference to the "J. Math. Chem." in one > of the postings to CCL. Since this journal is not > available here, could someone please send me some > information who is the publisher/editor, and how to > contact him? > Answers: > From jordi@stark.udg.es Thu Feb 16 19:43:00 1995 > > > Dear Dr. Homeier, > > I've got some information on the Journal of Mathematical > Chemistry, because we receive it in the library. > > Editors-in-chief: > > * P.G. Mezey > Dept. of Chemistry and Dept. of Mathematics > Univ. of Saskatchewan > Saskatoon, Saskatchewan > Canada S7N 0W0 > Fax: 1-306-966 4730 > > * N. Trinajstic > Rugjer Boskovic Institute > P.O. Box 1016 > 41001 Zagreb > Croatia > > It is edited by: > > * J.C. Baltzer AG Science Publishers > Wettsteinplatz 10 > CH-4058 Basel > Switzerland > Tel: 41-61-691 89 25 > Fax: 41-61-692 42 62 > E-mail: na.baltzer@na-net.ornl.gov > > An estimate of the institutional price is ca. US$ 837 > > Hope this helps, > > Jordi > > > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > Jordi Mestres _/ _/ _/ _/_/_/_/ > Institut de Quimica Computacional _/ _/ _/ _/ > Universitat de Girona _/ _/ _/ _/ _/ _/ _/_/ > Albereda 3-5 _/ _/ _/ _/ _/ _/ > 17071 Girona, CATALONIA (Spain) _/_/_/ _/ _/ _/ _/_/_/_/ > > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > > From campos@OREGON.UOREGON.EDU Thu Feb 16 20:34:22 1995 > > Dear Dr. Homeier > > The editors of J. Math Chem. are > > P. G. Mezey > Department of Chemistry > University of Saskatchewan, > Saskatoon S7N 0W0 > Canada > > and, > > N. Trijajstic, > Rugjer Boskovic Institute > P.O. Box 1016 > 41001 Zagreb, > Croatia > > Sincerely, > > Gerardo Soto-Campos > UofOregon > Eugene OR, USA > From servant@cassis-gw.univ-brest.fr Thu Feb 16 16:40:13 1995 Received: from mailimailo.univ-rennes1.fr for servant@cassis-gw.univ-brest.fr by www.ccl.net (8.6.9/930601.1506) id QAA04085; Thu, 16 Feb 1995 16:16:14 -0500 Received: from cassis-gw.univ-brest.fr by mailimailo.univ-rennes1.fr (8.6.9/20Sep94) with SMTP id WAA20911 for ; Thu, 16 Feb 1995 22:14:23 +0100 Received: by cassis-gw.univ-brest.fr (4.1/210992); Thu, 16 Feb 95 22:15:29 +0100 Date: Thu, 16 Feb 95 22:15:29 +0100 From: servant@cassis-gw.univ-brest.fr (Gwenael Servant) Message-Id: <9502162115.AA14267@cassis-gw.univ-brest.fr> To: chemistry@ccl.net Subject: Help for Mopac Hello dear Netters, I have tried to get MOPAC for DOS and for LINUX by www.ccl.net but the DOS zipped version has a bug (I can't unzip it) and the Linux version doesn't work on my system. Could someone please tell me where I can get a good version of MOPAC for -a DOS system -a LINUX system -or a SUN4 system Thamks a lot Gwenael SERVANT servant@cassis-gw.univ-brest.fr From TOMKINSON_NP@fisonspharm.co.uk Thu Feb 16 12:45:13 1995 Received: from bit158.fisonspharm.co.uk for TOMKINSON_NP@fisonspharm.co.uk by www.ccl.net (8.6.9/930601.1506) id MAA29792; Thu, 16 Feb 1995 12:45:06 -0500 Received: from mr.fisonspharm.co.uk by BIT158.FISONSPHARM.CO.UK (PMDF V4.3-10 #6968) id <01HN4JCRLCA80014NB@BIT158.FISONSPHARM.CO.UK>; Thu, 16 Feb 1995 17:45:09 +0000 (GMT) Received: with PMDF-MR; Thu, 16 Feb 1995 17:41:56 GMT MR-Received: by mta IOS; Relayed; Thu, 16 Feb 1995 17:42:08 +0000 MR-Received: by mta BIT158; Relayed; Thu, 16 Feb 1995 17:44:46 +0000 Alternate-recipient: prohibited Disclose-recipients: prohibited Date: Thu, 16 Feb 1995 17:31:00 +0000 (GMT) From: Nicholas Tomkinson Subject: charges again To: chemistry%ccl.net%smtp%WPC%IOS@mr.fisonspharm.co.uk Message-id: <01HN4JCVE8WM0014NB@mr.fisonspharm.co.uk> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Posting-date: Thu, 16 Feb 1995 17:34:00 +0000 (GMT) Importance: normal Priority: normal X400-MTS-identifier: [;65147161205991/334947@UKC] A1-type: MAIL Hop-count: 3 Status: RO My apologies for the control characters in my mail message. I think the problem lies with editing the file on the SG but having to mail the thing on the vax. I shall try and send it again. sigh Nick From herbert.homeier@rchs1.chemie.uni-regensburg.de Thu Feb 16 15:38:53 1995 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.6.9/930601.1506) id PAA03479; Thu, 16 Feb 1995 15:38:31 -0500 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA06113 (5.65c/IDA-1.4.4 for ); Thu, 16 Feb 1995 21:38:20 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA06612; Thu, 16 Feb 95 21:39:53 +0100 Date: Thu, 16 Feb 95 21:39:53 +0100 From: Herbert Homeier (t4720) Message-Id: <9502162039.AA06612@rchs1.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: Summary: J. Math. Chem: Status: RO Dear CCLers, Many thanks to all who replied to my question. My post was: > I saw some reference to the "J. Math. Chem." in one > of the postings to CCL. Since this journal is not > available here, could someone please send me some > information who is the publisher/editor, and how to > contact him? > Answers: > From jordi@stark.udg.es Thu Feb 16 19:43:00 1995 > > > Dear Dr. Homeier, > > I've got some information on the Journal of Mathematical > Chemistry, because we receive it in the library. > > Editors-in-chief: > > * P.G. Mezey > Dept. of Chemistry and Dept. of Mathematics > Univ. of Saskatchewan > Saskatoon, Saskatchewan > Canada S7N 0W0 > Fax: 1-306-966 4730 > > * N. Trinajstic > Rugjer Boskovic Institute > P.O. Box 1016 > 41001 Zagreb > Croatia > > It is edited by: > > * J.C. Baltzer AG Science Publishers > Wettsteinplatz 10 > CH-4058 Basel > Switzerland > Tel: 41-61-691 89 25 > Fax: 41-61-692 42 62 > E-mail: na.baltzer@na-net.ornl.gov > > An estimate of the institutional price is ca. US$ 837 > > Hope this helps, > > Jordi > > > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > Jordi Mestres _/ _/ _/ _/_/_/_/ > Institut de Quimica Computacional _/ _/ _/ _/ > Universitat de Girona _/ _/ _/ _/ _/ _/ _/_/ > Albereda 3-5 _/ _/ _/ _/ _/ _/ > 17071 Girona, CATALONIA (Spain) _/_/_/ _/ _/ _/ _/_/_/_/ > > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > > From campos@OREGON.UOREGON.EDU Thu Feb 16 20:34:22 1995 > > Dear Dr. Homeier > > The editors of J. Math Chem. are > > P. G. Mezey > Department of Chemistry > University of Saskatchewan, > Saskatoon S7N 0W0 > Canada > > and, > > N. Trijajstic, > Rugjer Boskovic Institute > P.O. Box 1016 > 41001 Zagreb, > Croatia > > Sincerely, > > Gerardo Soto-Campos > UofOregon > Eugene OR, USA > From servant@cassis-gw.univ-brest.fr Thu Feb 16 16:16:38 1995 Received: from mailimailo.univ-rennes1.fr for servant@cassis-gw.univ-brest.fr by www.ccl.net (8.6.9/930601.1506) id QAA04085; Thu, 16 Feb 1995 16:16:14 -0500 Received: from cassis-gw.univ-brest.fr by mailimailo.univ-rennes1.fr (8.6.9/20Sep94) with SMTP id WAA20911 for ; Thu, 16 Feb 1995 22:14:23 +0100 Received: by cassis-gw.univ-brest.fr (4.1/210992); Thu, 16 Feb 95 22:15:29 +0100 Date: Thu, 16 Feb 95 22:15:29 +0100 From: servant@cassis-gw.univ-brest.fr (Gwenael Servant) Message-Id: <9502162115.AA14267@cassis-gw.univ-brest.fr> To: chemistry@ccl.net Subject: Help for Mopac Status: RO Hello dear Netters, I have tried to get MOPAC for DOS and for LINUX by www.ccl.net but the DOS zipped version has a bug (I can't unzip it) and the Linux version doesn't work on my system. Could someone please tell me where I can get a good version of MOPAC for -a DOS system -a LINUX system -or a SUN4 system Thamks a lot Gwenael SERVANT servant@cassis-gw.univ-brest.fr From h.rzepa@ic.ac.uk Thu Feb 16 17:34:06 1995 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id RAA05491; Thu, 16 Feb 1995 17:24:02 -0500 Received: from cscmgb.cc.ic.ac.uk (actually sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Thu, 16 Feb 1995 22:23:18 +0000 Received: from anxa03 by cscmgb.cc.ic.ac.uk (931110.SGI/4.0) id AA06968; Thu, 16 Feb 95 22:23:07 GMT X-Sender: rzepa@sg1.cc.ic.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 16 Feb 1995 22:33:54 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa, Henry) Subject: Announce: Electronic Conference on Trends in Organic Chemistry ECTOC: Electronic Conference on Trends in Organic Chemistry =========================================== The first Electronic conference for discussing Trends in Organic Chemistry will be held during 12-23 June 1995 on the Global Internet using electronic mail and the World-Wide Web as delivery mechanisms, and organised under the guidance of an international scientific committee. This pioneering forum offers a novel, low cost and near-instant mechanism for discussing chemistry, with features such as full colour structure diagrams, "clickable" reaction schemes, rotatable 3D molecular images, key-word searches of conference proceedings, and access to a conference "molecular hyperglossary". See issue 3, 1995 of Chemical Communications for further details and J. H. Krieger and D. L. Illman, Chem. & Eng. News, 1994, 1994 (December 12), 29 for details of the previous ECCC conference organised along similar lines. Contributions will take the form of a number of invited Keynote papers, together with submitted papers, conference posters, and electronic mail discussions, in all areas of contemporary organic chemistry, including synthesis, structure, mechanism, physical organic, new materials, bio-organic and computational studies. Papers and posters will be subjected to the peer review process and we expect will be published on a conference CD-ROM which will be abstracted by Chemical Abstracts. The deadline for submission of abstracts of papers or posters is April 28, 1995. Conference information and details of how to submit contributions are available by the following mechanisms; 1. Sending an electronic mail to listserver@ic.ac.uk with the single line message; info ectoc 2. Connecting to the following World-Wide Web location using a browser such as Mosaic or Netscape; http://www.ch.ic.ac.uk/ectoc/ 3. By anonymous ftp file transfer of the file ectoc.txt in the directory pub on the server ftp.ch.ic.ac.uk ----------------------------------------------------------------------------- Please pass this message along to any organic chemists who might not subscribe to the computational chemistry list. Dr Henry Rzepa, Dept. Chemistry, Imperial College, London, SW7 2AY. Tel: +44 171 594 5774. Fax: +44 171 594 5804. E-mail: rzepa@ic.ac.uk URL: http://www.ch.ic.ac.uk/rzepa.html Sent using Eudora 2.1.1 From mrigank@imtech.ernet.in Thu Feb 16 20:40:16 1995 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.9/930601.1506) id TAA07885; Thu, 16 Feb 1995 19:54:51 -0500 Received: (from root@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id GAA08997 for chemistry@ccl.net; Fri, 17 Feb 1995 06:24:18 +0530 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA22865; Fri, 17 Feb 95 01:04:52+050 Message-Id: <9502162004.AA22865@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Thu, 16 Feb 95 22:42:01 +0530 Date: Thu, 16 Feb 95 22:42:01 +0530 From: Mrigank To: chemistry@ccl.net Subject: Evolutionary relation between sequences ?? Hi I am looking for program to find out evolutionary relationship between two protein sequences/motifs or find a connection of sequence with a sequence database. The program should be able to give closeness/distance in reference to evolution should be I guess PAPA [or some such name] by Dolittle's group can do this. Can any one give pointers to this or any other s/w. Thanks Mrigank ---- /Mrigank \/ Phone +91 172 690557 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 690585 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From gwaltney@qtp.ufl.edu Thu Feb 16 20:47:55 1995 Received: from crunch for gwaltney@qtp.ufl.edu by www.ccl.net (8.6.9/930601.1506) id UAA08250; Thu, 16 Feb 1995 20:33:45 -0500 Received: from red11 by crunch (5.x/4.11) id AA12639; Thu, 16 Feb 1995 20:33:38 -0500 From: "Steve Gwaltney" Received: by red11 (5.x/4.11) id AA00497; Thu, 16 Feb 1995 20:33:36 -0500 Date: Thu, 16 Feb 1995 20:33:36 -0500 Message-Id: <9502170133.AA00497@red11> To: CHEMISTRY@ccl.net Subject: Re: CCL:ACES2 question Cc: gwaltney@qtp.ufl.edu, jkong@is.dal.ca X-Sun-Charset: US-ASCII > For some reason, I can't get CCSD run with ACES2. Here is the error > message: > > Could not load program xvprops > Symbol #NREAD in bsh is undefined > > Error was: Exec format error Without seeing the input file, I can only guess at the cause of the problem. Were you trying to run a property calculation? Because xvprops is the property integral module. Recently its name was changed from xvprop because the name xvprop caused a confilct with one of the X11 routines. It is quite possible that somehow the name of your property integral module did not get changed. To solve the problem, go to the directory where ACES II is installed, and do one of the following: You can move xvprop to xvprops with the command mv xvprop xvprops or, alternately, you can just create a soft link with ln -s xvprop xvprops This should fix your problem. If it does not, either contact me or drop a note to aces2@qtp.ufl.edu describing the problem. Actually, that address can be used for any questions about or problems with ACES II. Steve Steven Gwaltney gwaltney@qtp.ufl.edu If the NSF actually listened to Quantum Theory Project me, we would all be better off. University of Florida