From lim@rani.chem.yale.edu Tue Feb 21 04:51:40 1995 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by www.ccl.net (8.6.9/930601.1506) id EAA13090; Tue, 21 Feb 1995 04:08:13 -0500 Received: by rani.chem.yale.edu; Tue, 21 Feb 95 04:08:13 -0500 From: Dongchul Lim Message-Id: <9502210908.AA23358@rani.chem.yale.edu> Subject: conformational isomers To: chemistry@ccl.net (Computational Chemistry) Date: Tue, 21 Feb 95 4:08:12 EST X-Mailer: ELM [version 2.3 PL11] Is there a simple way of testing if two given conformational isomers are equivalent? E.g., how can you know the gauche (+) conformer of n-butane is equivalent to the gauche (-) conformer? My idea is 1) superimpose the two conformers. 2) if they are not superimposed, superimpose the one conformer and the mirror image of the other. Any ideas? -D.L. From thep@risc1.lrm.fi.cnr.it Tue Feb 21 05:01:37 1995 Received: from risc1.lrm.fi.cnr.it for thep@risc1.lrm.fi.cnr.it by www.ccl.net (8.6.9/930601.1506) id EAA13108; Tue, 21 Feb 1995 04:13:16 -0500 Received: by risc1.lrm.fi.cnr.it (AIX 3.2/UCB 5.64/4.03) id AA23333; Tue, 21 Feb 1995 10:03:18 +0100 From: thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) Message-Id: <9502210903.AA23333@risc1.lrm.fi.cnr.it> Subject: Information on MolScript (summary) To: chemistry@ccl.net Date: Tue, 21 Feb 1995 10:03:17 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 8529 Dear Colleague, Here is the file obtain.info written by Per Kraulis (the Author of MolScript). Contact him for further information... Your sincerely, Pornthep ----------------------------------------------------------------------------- Thanks for your interest in my program MolScript. This is a description of how to obtain the program. * Print, read and sign the license agreement. * Send the signed hard-copy license agreement to me (address below). * Choose one of the alternatives below for means of distribution and act accordingly. * There is no fee for academic researchers. Of course, I do expect proper recognition in publications (see license). * Companies must pay a fee of 2,000 pound sterling (GBP). Otherwise, the conditions are basically the same as for academics. Alternative 1: e-mail using uuencode ------------------------------------ The e-mail distribution consists of an uuencoded compressed tar file (about 800 KB) containing source code, documentation, makefiles and example input files. The file was made on an SGI system, but can be handled on SUN, ULTRIX and ESV machines (and probably other UNIX systems as well). When you have put the signed license agreement in the post, you may contact me (e-mail see below) to tell me so, and I will e-mail back the distribution. Alternative 2: anonymous FTP ---------------------------- The anonymous FTP distribution consists of a compressed tar file (molscript.tar.Z, about 580 KB) containing source code, documentation, makefiles and example input files. The file was made on an SGI system, but can be handled on SUN, ULTRIX and ESV machines (and probably other UNIX systems as well). When you have put the signed license agreement in the post, you may contact me (e-mail see below) to give me the Internet number (name address is usually not enough) for the machine that I should transfer the MolScript distribution file to. If you do not have anonymous FTP set up on your machine, then another account may be used. However, then I will have to have the password for that account. In such a case, use fax to send account and password to me, which is more secure than sending it over the net. I promise not to use this account for anything else than transferring MolScript. There is currently no way for you to access my FTP site. Alternative 3: from a friend ---------------------------- If you know of someone that you can easily get the MolScript program from, then you may do so if and only if the following conditions hold: 1) You have read, signed and posted the license agreement to me. 2) You will let me know of what you are doing and the name of the person that you are getting the program from. 3) You tell the person you are getting the program from that you have signed the license, and that you are telling me (PK) about what you are doing. 4) The person you are getting the program from is perfectly willing to spend time doing this, and you are not imposing yourself on him/her. If in doubt, contact me instead. If you get the program in this way, be sure to get both the forlib and molscript directories, since both are needed to recompile the program. Not an alternative: tape ------------------------ I no longer distribute MolScript via tape. It simply takes too much time for me to handle tapes. Exceptions to this can be made only in extreme circumstances, and only after discussion with me. General information ------------------- The program is written in pure Fortran 77. Only the Silicon Graphics IRIS version is supported with a makefile. The source code was written to be as system-independent as possible. It should not be too difficult to port the MolScript program to other systems, provided there is a decent Fortran 77 compiler and run-time system. There are makefiles and forlib procedures for SUN and ULTRIX, although no guarantees are given; these are not kept up to date anymore. However, the source code and makefiles will most probably work for other systems as well, such as ESV and IBM RS6000. For VAX/VMS, the i/o logical units in the source code will have to be changed. This you will have to do yourself. The Raster3D package is not part of the distribution. This package you will have to fetch yourself from the anonymous ftp site stanzi.bchem.washington.edu (IP 128.95.12.38). Yours sincerely, Per Kraulis ------------------------------------------------------------------ Per Kraulis, Ph.D. Pharmacia Biopharmaceuticals, N62:5 phone: +46 (8) 695 78 34 S-112 87 Stockholm fax: +46 (8) 695 40 82 SWEDEN e-mail: per.kraulis@sto.pharmacia.se ------------------------------------------------------------------ "Nothing is more difficult than simplicity." Unattributed. ------------------------------------------------------------------ and here the mentioned license.academic file ... License for MolScript v1.4 ========================== This is a license for MolScript, academic software version 1.4 (copyright (C) 1993 Per Kraulis), a program for creating plots in PostScript format of molecular structures. This license is to be signed by your institution (hereinafter referred to as the "LICENSEE"), and returned to Per Kraulis (hereinafter referred to as the "LICENSOR"). The computer program, including source code, documentation and example input files, as well as any modifications or derivative works made by the LICENSEE, are hereinafter referred to collectively as the "SOFTWARE". Terms 1. A non-exclusive, non-transferable license is granted to the LICENSEE to install and use the SOFTWARE on an appropriate computer system or systems located at LICENSEE's institution to which the LICENSEE has authorized access. Use of the SOFTWARE is restricted to LICENSEE and collaborators at his institution who have agreed to accept the terms of this license. 2. 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The LICENSEE shall not disclose in any form either the delivered SOFTWARE or any modifications or derivative works based on the SOFTWARE to third parties without prior written authorization from the LICENSOR. 6. If the LICENSEE receives a request to furnish all or any portion of the SOFTWARE to any third party, he will not fulfill such a request, and will refer it in writing to the LICENSOR. 7. The LICENSEE agrees that the SOFTWARE is furnished on an "as is" basis, and that the LICENSOR in no way warrants the SOFTWARE or any of its results and is in no way liable for any use LICENSEE makes of the SOFTWARE. 8. LICENSEE agrees that any reports or publications of results obtained with the SOFTWARE will acknowledge its use by an appropriate citation. This would refer to the following publication: Per J. Kraulis, "MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures", Journal of Applied Crystallography (1991) vol 24, pp 946-950. 9. The terms of this license shall not be limited in time. To evidence your acceptance of the terms and conditions set forth above, please sign in the indicated space and return this letter to the LICENSOR. Per Kraulis, PhD _________________________ Date _________________________________________________________________ Signature _________________________________________________________________ Name _________________________________________________________________ Institution _________________________________________________________________ Address _________________________________________________________________ FAX, e-mail ------------------------------------------------------------------------------- From TOMKINSON_NP@fisonspharm.co.uk Tue Feb 21 05:51:41 1995 Received: from bit158.fisonspharm.co.uk for TOMKINSON_NP@fisonspharm.co.uk by www.ccl.net (8.6.9/930601.1506) id FAA13360; Tue, 21 Feb 1995 05:04:52 -0500 Received: from mr.fisonspharm.co.uk by BIT158.FISONSPHARM.CO.UK (PMDF V4.3-10 #6968) id <01HNB2PTQWF400020N@BIT158.FISONSPHARM.CO.UK>; Tue, 21 Feb 1995 10:04:04 +0000 (GMT) Received: with PMDF-MR; Tue, 21 Feb 1995 10:01:29 GMT MR-Received: by mta IOS; Relayed; Tue, 21 Feb 1995 10:01:53 +0000 MR-Received: by mta BIT158; Relayed; Tue, 21 Feb 1995 10:03:43 +0000 Alternate-recipient: prohibited Disclose-recipients: prohibited Date: Tue, 21 Feb 1995 09:57:00 +0000 (GMT) From: Nicholas Tomkinson Subject: charges again To: chemistry%ccl.net%smtp%WPC%IOS@mr.fisonspharm.co.uk Message-id: <01HNB2PXAP4M00020N@mr.fisonspharm.co.uk> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Posting-date: Tue, 21 Feb 1995 09:58:00 +0000 (GMT) Importance: normal Priority: normal X400-MTS-identifier: [;92100112205991/338297@UKC] A1-type: MAIL Hop-count: 3 Dear all, Once more with feeling. Thanks to Konrad for helping reformat this. Thank you to all who posted responses. Based upon the response and a second trawl through the archive I shall be using MNDO for my comfa charges in future. I shall probably still use AM1 for optimisation. (The quality of charges from each method is assessed in a paper by Carlos Aleman published in J.Comp.Chem. vol 14 799-808 (1993).) I tend to agree with Konrad Koehler who suggests that random errors in charge schemes will just add noise to a CoMFA analysis. This will be less than the error introduced by being inconsistent I should think. ################################################################################ I have two statements and a question for you. 1) My experience of fitting charges using CHELPG to ab initio results indicates that the charges you get vary somewhat due to conformation (10-20%). As I'm using MD I just use an "average charge". 2) As I'm sure many others will tell you Mulliken charges bear little resemblance to the charges produced by any of the ESP fit methods. This can have a pretty significant effect on your calculation. I looked at MNDO, AM1, PM3 and ab initio (up to 6-31G*). Basicly, MNDO Mulliken analyses are closest to the ESP fits of the ab initio calcs. AM1 produces larger 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 might be able to save yourself some time by reducing the mesh of points where you are doing the fitting to cover those parts of the molecule that are of real interest or where there is significant charge seperation. 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. P.S. In defense of MNDO. I started out using the other two methods (AM1 and PM3) and found that they didn't do nearly as good a job at evaluating 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. AM1 does better but is still too attractive. MNDO is a little too repulsive but is still the closest fit to ab initio results. Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario (613) 541-6000 X6175 ############################################################# ################### Nicholas I am often concerned with validity of partial atomic charges. The method I've settled on for small molecules involves full geometry optimization using AM1 (the later versions handle sulfur), then resubmitting for an ESP-MNDO calculation with no geometry optimization (there's a hiccup with this in that my version of sybyl generates a .dat file specifying full geometry optimization regardless of what one wants, so I submit the MNDO ESP file on "hold for later" without specifying "user other MOPAC" [this generates the proper .dat file], then outside sybyl do a "RunMopac etc"). My concern about using MNDO for the geometry optimization as well is related to inaccuracies in the charge calculations which I thought could arise in systems with partial double bonds which MNDO might not recognize too well, giving "twisted" groups which should be planar (and undergoing resonance). The slowness of ESP is a problem but I believe recently is has been sped up considerably. I would put more trust in charges derived from this than from PM3 Mulliken, although I too have also read that consistent use of a certain method, rather than the method itself, may be more important for CoMFA/Docking etc. CoMFA is potentially a great method, although I would like to see the ability to incorporate hydrophobic fields (which can be done by interfacing to HINT, by G. Kellogg) and flexible molecules should be used with caution. People have suggested various dielectric constants for emulating a protein interior (which is I suppose what you are after), varying from 4 to something in the 30s, as an alternative to a distance-dependant dielectric, but I am unaware of one being a "clear winner". As a chemist with little time recently for modelling, I would like to validate the above, which are essentially "hunches"; please can I see your answers if you don't post them to the net. +----------------------------------------------------------------------Dr Jonathan Ball CSIRO, Division of Animal Health Private Bag 1, Parkville, Victoria 3052 Australia Internet email: baell@mel.dah.csiro.au Tel: +61 3 342-9782 Fax: +61 3 347-4042 ______________________________________________________________________ ################################################################################ Dear Dr. Tomkinson, I read with interest your comments about semiempirical charges for CoMFA work. I have a few comments that may be helpful in the context of your questions: - PM3 is known to be unreliable for charges. The reasons for this are relatively well-known, but I would certainly NOT depend on these charges for analyses such as you are carrying out. While certainly not perfect, I think that AM1 is usually considered to be more reliable than PM3 for quantities related to analysis of the molecule's wavefunction. AM1 can be found in many places, especially the various versions of AMPAC amd MOPAC now available. The AM1 reference is: Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902. - I would NEVER recommend using Mulliken-derived charges with a minimal basis set semiempirical method like AM1 or PM3. The basis set dependency of Mulliken makes the application of this method essentailly invalid. I hope that when you WROTE "Mulliken" you MEANT "Coulson". This is the technique that is used by default in both AMPAC and MOPAC and these charges are those that are reported in the OUT and ARC files resulting from these programs. References to the Coulson approach are: 1) Armstrong, D. R.; Perkins P. G.; Stewart, J. J. P. J. Chem. Soc., Dalton 1973, 838; 2) Pople, J. A.; Beveridge, D. L. Approximate Molecular Orbital Theory; McGraw-Hill: New York, 1970; pp 67. - Both MNDO and AM1 have sulfur parameters in modern implementations of the methods. - ESP is a good charge method and may run much faster in some programs than others. You should look around. Cheers, Andy Holder =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-=3D-=3D- ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry Internet Addr: aholder@cctr.umkc.edu Univ. of Missouri - Kansas City Phone Number: (816) 235-2293 Spencer Chemistry, Room 315 FAX Number: (816) 235-5502 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-=3D-=3D- ################################################################################ Hi Nicholas, Partial charges can be calculated from wave functions (semiemp or ab initio) by the Mulliken or ESP, among other methods. The ESP method is better 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 dipoles calculated from ESP charges (it doesn't happen with Mulliken). The trends are for many conformations of 20 - 50 atoms molecules. Now, if you need something faster that also reproduces dipoles you 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. Edgardo Garcia Univ. of Colorado BOULDER CO USA ################################################################################ Subject: Re: CCL:charges schemes with CoMFA 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. Bill Ross ################################################################################ Subject: Re: CCL:charges schemes with CoMFA See J. Med. Chem. 1993, 36, 2390. I that paper, I performed a CoMFA on ACE inhibitors using PM3 charges. The original manuscript in that series used the same alignment rule but Gast_Marsili charges. I did find that PM3 charges worked somewhat better. 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 charges which was comparable. 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 comfortable with the charge set (i.e. it gives reasonable looking charge distributions) and you are consistent in your treatment. CW ################################################################################ *Chris L. Waller, Ph.D. PHONE 919-541-7976* *Research Chemist FAX 919-541-5394* *waller@thor.herl.epa.gov * *Pharmacokinetics Branch (MD-74) * *ETD/HERL/USEPA * *Research Triangle Park, NC 27711 * * * *Disclaimer: Mention of trade names or products does not constitute* *endorsement by the United States Environmental Protection Agency. * ################################################################################ Subject: Re: CCL:charges schemes with CoMFA 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. Pertinent references: K. H. Kim, Y. C. Martin, Chapter in "QSAR: Rational Appraoches on the Design of Bioactive Compounds", C. Silipo and A. Vittoria, Eds., Elsevier, Amsterdam.", 1991 "Evaluation of Electrostatic and Steric Descriptors for 3D-QSAR: The H+ and CH3 Probes Using Comparative Molecular Field Analysis (CoMFA) and the Modified Partial Least Squares Method" pp 151-154. Ki. H. Kim and Yvonne C. Martin, J. Org. Chem., 56, 2723-2729, 1991, =D2Direct Prediction of Linear Free Energy Substituent Effects from 3D Structures Using Comparative Molecular Field Analysis. 1. Electronic Effects of Substituted Benzoic Acids=D3. 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 from 3D Structures Using a Comparative Molecular Field Analysis )CoMFA) Approach=D3. In unpublished work, we also found that AM1 is just fine for phenols and anilines, provided that one uses the unprotonated form for the structure optimization. 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> PS. The JOC article has the most comparisons. ################################################################################ Nick: My preference for CoMFA are ab initio 6-31G* ESP fitted charges.[1,2] If you only optimize bond lengths and valence angles and hold torsions fixed, these calculations are not as time consuming as you might think. 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 of magnitude faster than the Besler et al. method and more accurate. The method is currently parameterized for C,H,N,O,F, and Cl. The author (wang@irbm.it) is currently working on parameters for S and P. I suspect that the charges are more important than what dielectric constant you use. For a more radical approach, you might check out a recent paper by Klebe et al.[5].> I hope you find these references useful. Ciao, Konrad ------------------------------------------------------------------ | Konrad Koehler | Computational Chemistry Group | | internet: koehler@irbm.it | Department of Medicinal Chemistry | | | IRBM | | telephone: +39-6-910-93606 | Via Pontina Km. 30,600 | | fax: +39-6-910-93225 | 00040 Pomezia (Roma) | | | Italy | ------------------------------------------------------------------ (1) Allen, M. S.; La Loggia, A. J.; Dorn, L. J.; Martin, M. J.; Costantino, G.; Hagen, T. J.; Koehler, K. F.; Skolnick, P.; Cook, J. M. Predictive binding of b-carboline inverse agonists and antagonists via the CoMFA/GOLPE approach. J. Med. Chem. 1992, 35, 4001-4010. (2) Wong, G.; Koehler, K. F.; Skolnick, P.; Gu, Z.-Q.; Ananthan, S.; Schonholzer, P.; Hunkeler, W.; Zhang, W.; Cook, J. M. Synthetic and Computer Assisted Analysis of the Structural Requirements for Selective, High Affinity Ligand Binding to 'Diazepam-Insensitive' Benzodiazepine Receptors. J. Med. Chem. 1993, 36, 1820-30. (3) Ford, G. P.; Wang, B. A new approach to the rapid semiempirical calculation of molecular electrostatic potential based on the AM1 wave function: Comparison with ab initio HF/6-31G* results. J. Comput. Chem. 1993, 14, 1101-1111. (4) Wang, B.; Ford, G. P. Atomic charges derived from a fast and accurate method for electrostatic potentials based on modified AM1 calculations. J. Comput. Chem. 1994, 15, 200-207. (5) Klebe, G.; Abraham, U.; Mietzner, T. Molecular similarity indices in a comparqative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J. Med. Chem. 1994, 37, 4130-4146. ################################################################################ Nicholas: There have been publications confirming that CoMFA models are charge-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 models that are much the same as those using charges from semiempirical calculations. Phil Cruickshank ************************************************************* * Philip A. Cruickshank * * FMC Corporation, Agricultural Chemical Group * * Chemical Sciences Team * * P. O. Box 8, Princeton, NJ 08543 * * * * Telephone: (609)951-3646 Fax: (609)951-3835 * * e-mail: pacruickshank@fmc.com * ************************************************************* ################################################################################ Hi Nick, Hope things are fine at Loughborough. If you want a semi-emp method for charge calculations then the SAM1 method has had some good publicity lately, it handles phosphrous and sulphur better than AM1. Try talking 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... TTFN Andy -- ################################################################################ Structural and Computation Chemistry Group________chp1aa@uk.ac.surrey - JANET. Department of Chemistry___________________________phone_______+44-1483-259591. University of Surrey______________________________fax_________+44-1483-300803. Guildford,________________________________________ftp___________131.227.110.69 Surrey, GU2 5XH, UK_________________WWW http://www.chem.surrey.ac.uk/~chp1aa/ ################################################################################ ################################################################################ Subject: Re: charges schemes with CoMFA I will not discuss the impact of choosing partial charges in conformational analysis (CA), for two reasons: their magnitude (and "correctness") will influence the choice of your local minima [to the extent that empirical charges may give a different energy map than quantum-mechanical ones], 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 well with 631G* ESP charges - 0.94-0.96 R^2 for charge to charge correlation - 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 look for messages from Drs JJP Stewart, A Holder, E Zoebisch [and others...]. 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. Chris Waller has noted that PM3 gives better correlations than Gasteiger- Huckel, but I would point out that both models were correlating well in CoMFA. A paper I reviewed (I believe it is out in JMC) reported on the side that comparing AM1 vs Gasteiger-Marsili, they found no difference. In sum, as long as your CA results are ok, your CoMFA model is unlikely to yield significant differences by using different partial charges. As for the dielectric in CoMFA - I recently started using constant D instead of distance dependent one - again, it is unlikely to have a tremendous impact on the robustness/predictive/explanatory qualities of your model. --Tudor ************************************************************** * 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 * ************************************************************** ################################################################################# # On 10-FEB-1995, Tudor Oprea wrote in response to Nick Tomkinson's post: > 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 correlation - > better than STO-3G ESP for the same molecules [these with G92]. 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 reproducing 6-31G* ESPFIT charges) than the old MOPAC ESP charges. [1] Ford, G. P.; Wang, B. A new approach to the rapid semiempirical calculation of molecular electrostatic potential based on the AM1 wave function: 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 calculations. J. Comput. Chem. 1994, 15, 200-207. > 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=) > but for systems where no fancy electronic distribution occurs, MNDO or AM1 > can do the works. ... [rest of message deleted] The source of charges may not matter for systems like steroids or peptides, where most commonly used methods (including Gasteiger-Marsili) give reasonable charges. But in my experience, the source of charges does make a _big_ difference for systems such as aromatic heterocycles. We did a comparison of ESPFIT 6-31G* [3] vs. MNDO//PRDDO/ESPFIT [3] vs. Gasteiger-Marsili [unpublished]. The cross validated R2's were 0.71 vs. 0.65 vs. ~0.40 respectively. [3] Allen, M. S.; La Loggia, A. J.; Dorn, L. J.; Martin, M. J.; Costantino, G.; Hagen, T. J.; Koehler, K. F.; Skolnick, P.; Cook, J. M. Predictive binding of b-carboline inverse agonists and antagonists via the CoMFA/GOLPE approach. J. Med. Chem. 1992, 35, 4001-4010. The use of consistent charges will of course cancel systematic errors in the charges. However, if the errors are random and if the electrostatics (relative to sterics, hydrophobicity, etc.) are an important part of the correlation, then bad charges will produce bad correlations. Ciao, ------------------------------------------------------------------ | Konrad Koehler | Computational Chemistry Group | | internet: koehler@irbm.it | Department of Medicinal Chemistry | | | IRBM | | telephone: +39-6-910-93606 | Via Pontina Km. 30,600 | | fax: +39-6-910-93225 | 00040 Pomezia (Roma) | | | Italy | ------------------------------------------------------------------ ################################################################################# # Subject: Re: CoMFA charges> Hi - In regards to your question on charges. We have developed a method for obtaining partial charges that we call Charge Model 1 (CM1). The method is an empirical mapping of the Mulliken charges obtained by either AM1 or PM3. Of course, everyone has their favorite method for computing partial charges and there is no way to compare directly to experimental measurements. When developing CM1, we chose our method so that the dipole moment calculated from our partial charges reproduced the experimental dipole moment for that molecule as closely as possible. Calculating CM1 charges takes essentially no more time than the PM3 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 currently in press in the Journal of Computer- Aided Molecular Design (I unfortunately 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 been 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. David J. Giesen giesen@chemsun.chem.umn.edu ############################################################# From MCDI1ER1@fs1.ch.umist.ac.uk Tue Feb 21 09:51:45 1995 Received: from utserv.mcc.ac.uk for MCDI1ER1@fs1.ch.umist.ac.uk by www.ccl.net (8.6.9/930601.1506) id JAA16360; Tue, 21 Feb 1995 09:25:05 -0500 Received: from ursa.cns.umist.ac.uk by utserv.mcc.ac.uk with SMTP (PP); Tue, 21 Feb 1995 13:36:37 +0000 Received: from fs1.ch.umist.ac.uk by ursa.cns.umist.ac.uk with SMTP (PP); Tue, 21 Feb 1995 12:55:23 +0000 Received: from UMIST-CH-FS1/MAILQUEUE by fs1.ch.umist.ac.uk (Mercury 1.20); 21 Feb 95 12:55:24 GMT Received: from MAILQUEUE by UMIST-CH-FS1 (Mercury 1.20); 21 Feb 95 12:54:54 GMT From: Mr Eddie Rolph To: chemistry@ccl.net Date: Tue, 21 Feb 1995 12:54:49 GMT Subject: Chemistry through the Internet project X-Confirm-Reading-To: "Mr Eddie Rolph" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v3.21 Message-ID: <5CDA89F28BB@fs1.ch.umist.ac.uk> Internet Applications for Chemistry. There follows a brief questionnaire intended to both help me in my final year university project, and allow interested people get some insight into the general uses to which the internet is being put to in the chemistry field. Please exscuse any cross postings.The survey will take only a matter of minutes to fill out, but if enough people respond, then the results may prove very interesting reading.Information given will be treated as confidential,and stored on computer for acedemic use only. If you would like to receive a copy of the data obtained from this survey then please indicate so, and enclose your E-Mail address. Please post replies to:- Eddie.Rolph@UMIST.ac.uk Please do not post them to the mailing list. i. Which internet site(s) do you use most regularly?(Please include URL's if appropriate.) ii. How long have you been using these particular sites? iii. Do you think that any improvement could be made to the user- friendliness of these sites? iv. How reliable do you find the connections to these sites? v. Which do you consider the most important feature of the Internet? (a) The availability of information on a global basis, or (b) The ability to communicate ideas or results to colleagues around the world vi. Do you work for (a) An acedemic institution (b) A commercial company (c) A library or information unit (d) An information provider (e) Other - please specify vii. What is your position in this organisation? (Manager, Librarian, Undergrad, etc...) viii. In which country are you based? ix. Would you like to receive a copy of the survey results?(Insert E- Mail here if yes.) Thank you for your time in completing this questionnaire. Eddie Rolph. Final yr. Bsc (Computer-aided Chemistry), The University of Manchester Institute of Science and Technology, Sackville Street, Manchester. M60 1QD U.K. E-Mail Eddie.Rolph@UMIST.ac.uk or MCDI1ER1@ch.fs1.umist.ac.uk From lwalsh@aries.scs.uiuc.edu Tue Feb 21 10:57:35 1995 Received: from argus.cso.uiuc.edu for lwalsh@aries.scs.uiuc.edu by www.ccl.net (8.6.9/930601.1506) id KAA17329; Tue, 21 Feb 1995 10:00:28 -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 JAA75801 for <@argus.cso.uiuc.edu:chemistry@ccl.net>; Tue, 21 Feb 1995 09:00:28 -0600 Received: by aries.scs.uiuc.edu (931110.SGI/930416.SGI) for @argus.cso.uiuc.edu:chemistry@ccl.net id AA02216; Tue, 21 Feb 95 09:00:27 -0600 Date: Tue, 21 Feb 1995 09:00:27 -0600 (CST) From: Laura Walsh Subject: FLEXlm Summary with SCRIPT To: Computational Chemistry List Server Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Once more a summary, this time a bit more helpful. Here is a simple script that will count the number of simultaneous usages of a program managed by FLEXlm -- in this case SoftPC, but it works for Quanta/CHARMm and Cerius2 as well. Thanks VERY MUCH to the person who sent me this, whose name I unfortunately deleted when I edited the script for my purposes. Sometimes a starting point can really help and this did for me. Again, 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 ________________________________________________________________ #!/bin/sh ## ## Script to check the maximum # of SoftPC licenses checked ## out at any single time. Useful for estimating # of floating ## licenses that are needed. ## ## It can take an argument that is the log file to process. ## If no argument is given, the log-file is ## ## /usr/lib/SoftPC/FLEXlm/log-file ## ## by default. ## # Set default LOGFILE LOGFILE=/usr/lib/SoftPC/FLEXlm/log-file # See if they specified a different LOGFILE if [ $# = 1 ]; then LOGFILE=$1 fi # See if LOGFILE really exists if [ ! -f $LOGFILE ];then echo "No log file to check on this machine!" exit 1 fi MAXCOUNT=0 ## Max Number of licenses checked out at one time TMP=0 ## Temporary holder for number of licenses checked out BEG_DATE=`head -1 $LOGFILE | awk '{print $1}'` END_DATE=`tail -1 $LOGFILE | awk '{print $1}'` echo "" echo "\tReport for time period $BEG_DATE to $END_DATE" echo "\t-------------------------------------" echo "" echo "" for tran in `cat $LOGFILE | grep SoftPC_SGI | awk '{print $4}'` do if [ $tran = "OUT:" ]; then #echo $tran TMP=`expr $TMP + 1` if [ $TMP -gt $MAXCOUNT ]; then MAXCOUNT=$TMP fi elif [ $tran = "IN:" ]; then #echo $tran TMP=`expr $TMP - 1` fi done echo "Maximum number of concurrent SoftPC_SGI checkouts is " $MAXCOUNT From COYY@UNB.CA Tue Feb 21 11:31:37 1995 Received: from unb.ca for COYY@UNB.CA by www.ccl.net (8.6.9/930601.1506) id JAA16031; Tue, 21 Feb 1995 09:07:37 -0500 Received: from UNBVM1.CSD.UNB.CA by unb.ca (8.6.9/950124-08:07) id KAA25501; Tue, 21 Feb 1995 10:07:36 -0400 Received: from UNBVM1.CSD.UNB.CA by UNBVM1.CSD.UNB.CA (IBM VM SMTP V2R2) with BSMTP id 4755; Tue, 21 Feb 95 10:06:08 AST Received: from UNB.CA (NJE origin MUSIC@UNBVM1) by UNBVM1.CSD.UNB.CA (LMail V1.2a/1.8a) with BSMTP id 4754; Tue, 21 Feb 1995 10:06:07 -0400 Message-Id: <21FEB95.10906713.0228.MUSIC@UNB.CA> Date: Tue, 21 Feb 95 10:05:55 -0400 From: COREY To: Subject: CCL: 12th Canadian Symposium in Aug. X-Mailer: MUSIC/SP V3.1.1 12th Canadian Symposium on Theoretical Chemistry 12i me Symposium Canadien sur la Chimie Thorique Fredericton, 6-11 August/Aot 1995 Co-chairmen: William J. Meath and Ajit J. Thakkar The 12th Canadian Symposium on Theoretical Chemistry will be held August 6-11, 1995 at the Wu Conference Centre, University of New Brunswick, Fredericton, NB, under the co-chairmanship of William J. Meath (University of Western Ontario) and Ajit J. Thakkar (University of New Brunswick). The program will include invited papers and contributed posters in all areas of theoretical chemistry. The topics selected for emphasis are: * Structure, properties and dynamics of weakly interacting systems * Condensed phases from clusters to solids and from dynamics to bulk properties * Laser-molecule interactions: dynamics to spectroscopy * Kinetics and reaction dynamics * Molecular properties * Surfaces and interfaces * Materials design * Computer simulation and statistical mechanics * Quantum chemistry: methods and applications * Novel computational and mathematical techniques * Biochemical systems Invited Speakers Invited Speakers Session chairs J.M. Andre (Belgium) J.N. Murrell (England) R.J. Boyd A.D. Bandrauk (Canada) J. Oddershede (Denmark) T. Carrington, Jr. R.J. Bartlett (U.S.A.) S.D. Peyerimhoff (Germany) R.S. Dumont D.M. Bishop (Canada) P. Pyykko (Finland) I.P. Hamilton P. Botschwina (Germany) H.A. Rabitz (U.S.A.) W.G. Laidlaw P.W. Brumer (Canada) M.A. Ratner (U.S.A.) T.T. Nguyen-Dang D. Ceperley (U.S.A.) A. Rauk (Canada) J. Paldus E.R. Davidson (U.S.A.) S.A. Rice (U.S.A.) G.N. Patey C.E. Dykstra (U.S.A.) D.R. Salahub (Canada) R.A. Poirier J.T. Hynes (U.S.A.) P. Saxe (U.S.A.) S.M. Rothstein B. Jeziorski (Poland) H.A. Scheraga (U.S.A.) B.C. Sanctuary W.L. Jorgensen (U.S.A.) K.C. Showalter (U.S.A.) V.H. Smith, Jr. R.E. Kapral (Canada) J. Simons (U.S.A.) S.G. Whittington H.J. Kreuzer (Canada) D.W. Sumners (U.S.A.) J.S. Wright R.J. LeRoy (Canada) D.G. Truhlar (U.S.A.) M.C. Zerner W. Meyer (Germany) D.M. Wardlaw (Canada) T. Ziegler P.G. Mezey (Canada) K.B. Whaley (U.S.A.) W.H. Miller (U.S.A.) W. Yang (U.S.A.) D.J. Moore (Switzerland) Contributed papers are welcome in all areas of theoretical chemistry. All contributed papers will be given in poster format. For registration forms, contact the Conference Secretary, 12th CSTC, Department of Chemistry, University of New Brunswick, Fredericton, NB E3B 6E2, Canada. Fax: 506-453-4981. Internet: coyy@unb.ca From cletner@remcure.bmb.wright.edu Tue Feb 21 11:42:51 1995 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.9/930601.1506) id JAA16744; Tue, 21 Feb 1995 09:36:59 -0500 Received: by remcure.bmb.wright.edu (931110.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA07860; Tue, 21 Feb 95 09:28:56 -0800 Date: Tue, 21 Feb 1995 08:25:26 -0800 (PST) From: Charles Letner Subject: Re: CCL:summary of data analysis of protein structures To: Computational Chemistry List In-Reply-To: <9502201615.AA16703@iisc.ernet.in> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Sandeep and others, Thank you for compiling and posting your summary. There are two points that I think need to be concidered. > ... > 2) One could try to predict molecule's structure with force > filed calculations: too slow even for small molecules. > ( paramatrisation of MD programs takes a LOOOOOOOOOOOOOOOOOOOONG time. > only large companies, consortia etc. ( BIOSYM/SanDiego) can cope with > that.) > 3) MD is, in principle just an inadequate method. > why shold f.i. 2 H behave differently in the same distance from each > other when they have a different ditance along the backbone? > ... One of the basic assumptions of typical force fields is that you can Hooke's law to model bond lengths, ie: E = K(r-req)^2 where E is the energy, K is constant controlling the "stiffness" of the bond, r is the distance, and req is the ideal distance (K and req are the parameters for this term of the force field). Note that this is a parabola with it's minimum at req. This is different than reality. At long bond lengths this energy continually increases. In reality the bond breaks. Similar arguments can apply for the other typical terms. The point is that these force fields are ment to deal with systems that are close to the structure you are interested in modeling. Ie/ you can't take a long chain of amino acid residues and expect it to fold into some kind of meaningfull conformation. This is not to say in the limit of infinite time you might not find the conformation you are looking to find. Now if you have some previous knowledge of the conformation, ie/ high homology with another protein who's strucuture has been deteremined, you are playing a different game. SO, to use MM/MD to try and get the structure of a protein given no other info than it's primary sequence is probably an inaprorpriate use of the method. On the other hand, if you have some structural info it may be apropriate, ie/ you can at least make a "resonable" guess at what the strucutre is. > 4) if you work with ab initio-methods to fit data, they take an even > LOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOnger time to fit fro small molecules. True. However, I'm not sure that many people (is ANYONE) are trying to apply ab initio methods to protein structre. MAN would I love to have access to the machine that can run Gaussian on say 1000 atoms (the size of bpti, a small protein).... msec MD here I come! 8) A method that was not mentioned was genetic algorithms. I've seen some interesting results with GA's towards the problem of structure prediction. However, I can't say much else about them. It is probably worthwhile to mention Chow/Fasman, hydropothy plots, etc as more classical methods of structural prediction. Chow/Fasman did look at a large number of protein structures to come up with their empirical values. See Cantor and Schimmel (1980) volume 1 for more info. on these ideas. >Thiis board is still viewed by many as quantum chemistry and hence is >probably not widly followe by protein crystallographers.Subscribe to >bionet.xtallography on you nearest internet newstand and send them your >request. I expect this is true. But hey, there are a few renegade biochemist roaming this board... So stick around! Who know's maybe we'll convert all these chemist to biologist yet.... Oh ouch those flames are kill'n me! 8-) Or maybe it's the other way around. Anyhow, physicist say we are all evolving into physicist...... Bye, Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From tvolm@blue.weeg.uiowa.edu Tue Feb 21 13:51:43 1995 Received: from ns-mx.uiowa.edu for tvolm@blue.weeg.uiowa.edu by www.ccl.net (8.6.9/930601.1506) id MAA22145; Tue, 21 Feb 1995 12:58:01 -0500 Received: from blue.weeg.uiowa.edu by ns-mx.uiowa.edu (8.6.8.2/19950217.1) on Tue, 21 Feb 1995 11:58:00 -0600 id LAA00645 with ESMTP Received: by blue.weeg.uiowa.edu (8.6.9/940408) on Tue, 21 Feb 1995 11:57:55 -0600 id LAA208901 Date: Tue, 21 Feb 1995 11:57:51 -0600 (CST) From: volm timothy gerard To: chemistry@ccl.net Subject: biocatalysis Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The Center for Biocatalysis and Bioprocessing ( CBB ) will hold the Fourth Biocatalysis and Bioprocessing Conference at the The University of Iowa Memorial Union on May 15-16, 1995.The Conference will feature an introduction to the CBB, lectures by selected faculty members, graduate student presentations and a keynote address by Dr. Charles J. S. Sih of the University of Wisconsin. A large poster session will provide an opportunity for viewing and discussing current research. Industrial participants are invited to present posters on biocatalysis/bioprocessing research. Industrial participants who would like to present a scientific poster will receive complimentary registration. Abstract deadline is April 15, 1995. Please contact Ms. Beverly Palmer, Center for Biocatalysis and Bioprocessing, Oakdale Research Park, 2501 Crosspark Road - Suite C100, Iowa City, Iowa, 52242-5000 Phone (319)335-4900; FAX (319)335-4901. Meeting participants may visit the new CBB laboratory facility located in the Oakdale Research Park. Advanced registration is encouraged. The registration fee is $100, includes all conference meals and expenses except for travel and lodging. A $50 late registration fee will be added for those registering after May 1. From lnl@novo.dk Tue Feb 21 14:51:47 1995 Received: from sentry.novo.dk for lnl@novo.dk by www.ccl.net (8.6.9/930601.1506) id OAA23518; Tue, 21 Feb 1995 14:04:50 -0500 Received: from bisse.novo.dk by sentry.novo.dk; (5.65/1.1.8.2/28Sep94-0345PM) id AA06762; Tue, 21 Feb 1995 20:05:22 +0100 Received: by bisse.novo.dk (931110.SGI/930416.SGI.AUTO) for @sentry.novo.dk:chemistry@ccl.net id AA24570; Tue, 21 Feb 95 20:04:02 +0100 Date: Tue, 21 Feb 95 20:04:02 +0100 From: lnl@novo.dk (Leif Norskov) Message-Id: <9502211904.AA24570@bisse.novo.dk> To: chemistry@ccl.net Subject: Re: conformational isomers Dongchul Lim (lim@rani.chem.yale.edu) asked > Is there a simple way of testing if two given conformational isomers > are equivalent? > E.g., how can you know the gauche (+) conformer of n-butane is > equivalent to the gauche (-) conformer? > My idea is [ to superimpose the conformers ]... If speed is a problem (and it could well be - consider for example the matching of the protons in butane) then it might be advantageous to first compare the moments of inertia, which of course are invariant to atom labelling and rotation/translation, before proceeding with superpositioning. Cheers, Leif Norskov Novo Nordisk A/S Copenhagen Denmark lnl@novo.dk From eslone@osf1.gmu.edu Tue Feb 21 15:51:44 1995 Received: from osf1.gmu.edu for eslone@osf1.gmu.edu by www.ccl.net (8.6.9/930601.1506) id PAA25886; Tue, 21 Feb 1995 15:23:45 -0500 Received: by osf1.gmu.edu; (5.65/1.1.8.2/07Sep94-1001AM/GMUv1) id AB01796; Tue, 21 Feb 1995 14:44:57 -0500 Message-Id: <9502211944.AB01796@osf1.gmu.edu> Subject: New Program Upload To: chemistry@ccl.net Date: Tue, 21 Feb 1995 14:44:52 -0500 (EST) From: "J. Eric Slone" X-Mailer: ELM [version 2.4 PL24alpha5] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1002 I have just uploaded to www.ccl.net a new program I downloaded from Compuserve. In light of the Intel FPU problems, this Windows calculator program will work without error. It's a slide rule calculator, just like the good old Keuffel & Esser. For anyone who misses their old slide rule, this will be a welcome addition to your desktop. Enjoy! Eric ________________________________________________________________________________ J. Eric Slone George Mason University Department of Chemistry Fairfax, Virginia 22030-4444 Internet: eslone@gmu.edu Compuserve: 73757,2776 "True science teaches, above all, to Fax: (703) 751-6639 doubt, and to be ignorant." Pager: (202) 597-2373 Miguel de Unamuno Voice: (703) 461-7078 ________________________________________________________________________________ From ravishan@swan.wcc.wesleyan.edu Tue Feb 21 19:51:44 1995 Received: from swan.wcc.wesleyan.edu for ravishan@swan.wcc.wesleyan.edu by www.ccl.net (8.6.9/930601.1506) id TAA00903; Tue, 21 Feb 1995 19:46:19 -0500 Received: by swan.wcc.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA18300; Tue, 21 Feb 1995 19:50:45 -0500 Date: Tue, 21 Feb 1995 19:50:45 -0500 Message-Id: <9502220050.AA18300@swan.wcc.wesleyan.edu> From: "G. Ravishanker" To: chemistry@ccl.net Subject: Digitizing data Hi I am curious to know if anyone is knwledgeable in the current stat-of-the art in digitizing data. We used to use tablets and go through the painful process of clicking on each point. I want to know if there are software/hardware combinations available for Unix systems that make the task easier. Thanks in advance. Ravi -- **************************************************************************** * Ganesan Ravishanker Ph: (203) 685-2104 * * Coordinator of Scientific Computing, Fax:(203) 685-2211 * * Adjunct Associate Professor(Dept. of Chem.) * * Wesleyan University e-mail:ravishan@swan.wcc.wesleyan.edu * * Middletown, CT 06459. * **************************************************************************** From elewars@alchemy.chem.utoronto.ca Tue Feb 21 21:51:46 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.9/930601.1506) id VAA01901; Tue, 21 Feb 1995 21:18:59 -0500 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.9/8.6.9) id VAA16170 for chemistry@ccl.net; Tue, 21 Feb 1995 21:18:57 -0500 Date: Tue, 21 Feb 1995 21:18:57 -0500 From: "E. Lewars" Message-Id: <199502220218.VAA16170@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: TELLING IF TWO CONFORMERS ARE IDENTICAL Dongchul Lim asked how one can tell if two conformers are the same. This is a special case of how to tell if two isomers are really the same species. It seems to me a simple approach is (after looking to see that they are not obviously different) to have your program (MOPAC, GAUSSIAN etc) calculate the total internuclear repulsions. Two species that look the same and have the same internuclear repulsions (to 6 or more decimals--Hartrees) are, I would think, extremely unlikely not to be the same. Many comp. chem programs calculate internucl. repulsions; if a check job wn't give that number, then ask for a single-point calc. using a fast method like a semiempirical routine. The actual internuclear repulsin calc. is trivial. Errol Lewars =================== From steve@carbo.chem.binghamton.edu Tue Feb 21 22:51:45 1995 Received: from carbo.chem.binghamton.edu for steve@carbo.chem.binghamton.edu by www.ccl.net (8.6.9/930601.1506) id WAA02608; Tue, 21 Feb 1995 22:00:18 -0500 Received: by carbo.chem.binghamton.edu (931110.SGI/931108.SGI.ANONFTP) for chemistry@ccl.net id AA21122; Tue, 21 Feb 95 21:58:31 -0500 Date: Tue, 21 Feb 1995 21:55:33 -0500 (EST) From: Steven Schafer Subject: Q:Mathematica To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I seem to remember it being mentioned somewhere that there was a Mathematica notebook on Quantum Mechanics. Does anyone know where such a file may exist, or for that matter if there are any good chemistry notebooks. I will post a response if I get any answers. Thanks in advance, Steven Schafer S.U.N.Y. Binghamton Chemistry Department http://chemiris.chem.binghamton.edu:8080 Binghamton, New York USA From Karl.F.Moschner@urlus.sprint.com Tue Feb 21 10:37:01 1995 Received: from sprintf.merit.edu for Karl.F.Moschner@urlus.sprint.com by www.ccl.net (8.6.9/930601.1506) id KAA18218; Tue, 21 Feb 1995 10:36:58 -0500 Date: Tue, 21 Feb 1995 09:13:00 -0500 From: Karl.F.Moschner@urlus.sprint.com Message-ID: <"Tue Feb 21 09:13:41 199501*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: lim@rani.chem.yale.edu, chemistry@ccl.net Subject: CCL: RE: conformational isomers > Is there a simple way of testing if two given conformational > isomers are equivalent? > E.g., how can you know the gauche (+) conformer of n-butane is > equivalent to the gauche (-) conformer? > My idea is > 1) superimpose the two conformers. > 2) if they are not superimposed, superimpose the one conformer > and the mirror image of the other. > Any ideas? > -D.L. Sounds about right to me, but, if your program doesn't do so already, you should first provide a "standard" orientation such as placing the origin at the center of mass and orienting the molecule along the principal moment axes or dipoles, if you include charges. But, depending on your code, you may still have to consider reversed orientation, i.e., check if x1(a) = x1(b) or x1(a) = -x1(b), if the latter, reverse the orientation, ditto for y and z. Besides exact superposition, quick screens are the total energy, dipole (if you include charges), and moments. For larger molecules, end-to-end or selected interatomic distances afford quick checks. And, if you're checking a series of molecules, molecular weight or elemental composition are effective screens. It's suprising that some/many molecular mechanics packages do not support/generate "standard" orientations since it would be helpful not only for your problem but also as a start for CoMFA alignments. However, you could easily write your own starting from MOPAC or GAMESS subroutines, if you have them. There may also be a program/subroutine available from QCPE which you could modify. A few years ago I had modified the GAMESS subroutine for determining the principal moments to generate standard orienetations for Tripos "*.mol" files. It was very fast, requiring only a several seconds to reorient lysozyme on an SGI 4D/35. Unfortunately I no longer have the code and would be prohibited from redistributing it even if I did. My original interest was to subsequently compute the 3 principal cross-sectional areas, and/or solvent cross-sectioanl areas, to try to relate them to diffusivities but I didn't get that far. Good luck! _______________________________________________________________________ / \ | Comments are those of the author and not Unilever Research U. S. | | | | Karl F. Moschner, Ph. D. | | | | Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | | 45 River Road Phone: (201) 943-7100 x2629 | | Edgewater, NJ 07020 FAX: (201) 943-5653 | \_______________________________________________________________________/