From grzesb@asp.biogeo.uw.edu.pl Mon Oct 14 04:14:41 1996 Received: from asp.biogeo.uw.edu.pl for grzesb@asp.biogeo.uw.edu.pl by www.ccl.net (8.8.0/950822.1) id DAA21178; Mon, 14 Oct 1996 03:50:36 -0400 (EDT) Received: by asp.biogeo.uw.edu.pl (5.61/1.34) id AA15214; Mon, 14 Oct 96 09:07:31 +0100 Date: Mon, 14 Oct 96 09:07:31 +0100 From: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Message-Id: <9610140807.AA15214@asp.biogeo.uw.edu.pl> To: chemistry@www.ccl.net Subject: Summary:Shielding tensors for H Dear CCL Members, On Monday I asked a question about NMR shielding tensors for H atoms. It's hard to say but I've got only 2 (two) comments and few qurries to summarize. It seems that there is no comparative study about calculating shielding tensors for H atom. Thus DO EXIST publications on ^{11}B, ^{13}C, ^{15}N, ^{17}O, ^{19}F, ^{31}P .... Some people have calculated ^{1}H shielding tensors for few molecules but there was no systematic study on level of theory needed or basis set effects. It really puzzles me ... . For those who asked here is reference to work by Cheeseman et al: Cheeseman J.R., Trucks G.W., Keith T.A., Frisch M.J., J. Chem. Phys. Vol 104, No. 14 (8 April 1996) pp. 5497-5509. Thanks to Georg Schreckenbach and David E. Bernholdt who have shared their thoughts. Best regards, Grzegorz Bakalarski ICM|Warsaw University POLAND grzesb@asp.biogeo.uw.edu.pl ================== SUMMARY ================================== ----------------- Q U E R R Y ------------------------------------ Dear Netters, Recently I've read article by Cheeseman el al. about calculating absolute and relative NMR shielding tensors from different level of theory ( HF, MP2 and DFT) for different basis sets. The article is very interesting but the auhtors deal only with more "difficult cases - C, N and B atoms". I am interested in predicting NMR shielding tensors for H atoms in molecules ( it seems a easier case). Could anyone point me to similar article where I could find a systematic study of predicting NMR shielding tensors for H atom and it dependency on level of theory and basis set ? Any comments are also most welcomed! Best regards, ------------------ R E P L I E S ---------------------------------------- From schrecke@zinc.chem.ucalgary.ca Hi Grzegorz, I am always interested in the NMR stuff, therefore, I would be interested in your summary. Further, would you mind providing me with the reference for the article that you cite? I am not sure why H should be less difficult then C,N or B. In fact, I recall a presentation given recently by Don Chesnut where the conclusion was that H is MORE difficult than, e.g., Carbon. It depends, of course, on the meaning of "difficult". What Chesnut means is that the errors in calculated 1H shieldings (or shifts) are bigger than for say Carbon, if you consider the relative error w.r.t. the total shift range for the given nucleus. Chesnut has written a number of very readable reviews on NMR calculations, the most recent ones in "Reviews of Computational Chemistry" (I am not sure here) and in "Annual Reports on NMR Spectroscopy" Vol.29, G.A.Webb (Ed.), Academic Press, New York, 1994. I am not sure though whether your particular question is covered there. Yours, Georg ---------------- From: bernhold@npac.syr.edu My experience (not yet published) is that H shieldings are harder to get right (absolute, not sure about relative). I don't understand why this is; neither does an experimental colleague with extensive computational experience with shieldings. Part of it has to do with the small range and shifts typical for H, but I don't think that's the whole story. -- David E. Bernholdt | Email: bernhold@npac.syr.edu ______________________ D. Y. Chen and Ray Crawford asked for summary. ======================== T H E E N D ======================================== From ferenc@rchsg8.chemie.uni-regensburg.de Mon Oct 14 04:29:24 1996 Received: from comsun.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.8.0/950822.1) id DAA21188; Mon, 14 Oct 1996 03:53:32 -0400 (EDT) Received: from rchsg8.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA03051 (5.65c/IDA-1.4.4 for ); Mon, 14 Oct 1996 09:53:26 +0100 Received: by rchsg8.chemie.uni-regensburg.de (931110.SGI/URRZ-Sub-1.5-irix) (for CHEMISTRY@www.ccl.net) id AA09717; Mon, 14 Oct 96 09:52:37 +0200 Date: Mon, 14 Oct 96 09:52:37 +0200 From: ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9610140752.AA09717@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@www.ccl.net Subject: halomethanes Dear Netters: A few days ago I turned to the CCL with the following questions: Original request: > Dear Netters: > > I would like to calculate the optimized structures and > normal modes for a set of related compounds (halomethanes). > > Cl2-C-F2 (Dichlorodifluoromethane) > / \ > Cl-C-F2* Cl2-C-F2+ > (radical) (cation) > / \ > Cl-C-F2+ C-F2 > (cation) (carbene) > \ > C-F > >What type of basis-set would you recommend, that >treats all of these species in a balanced way? > >My idea was to use polarization and diffuse functions >to catch the ionic or radical character of these species. > >I belive, that Hartree-Fock (HF) will do a poor job for some >of these molecules and one has to include electron-correlation >even during optimization! Do you think that it is sensible >to start from a HF minimum structure and to reoptimze with MP2? > >Calculating normal modes with MP2 will be quite expensive >in terms of CPU and disk usage! Any idea about the "precision" >that can be expected from such a calculation? > >I have little experience with the calculation of ionic or >radical species and every comment, hint, or suggestion >is very much appreciated! I will summarize all the responses. I think it is time to summarize the replies. I am very grateful for the valuable information I obtained from: Dr. Luigi Cavallo, Dr. Peter R. Schreiner, Errol Lewars, and Russell D. Johnson III. Their original messages will be appended to this posting. Basically, I decided to compare three levels of theory (HF and Post-HF) for the problem stated in the original posting: 1) QCISD/6-311G(d,p) 2) MP2/6-311++G(d,p) 3) B3LYP/cc-pVTZ The results of these calculations will be compared to available experimental data (geometries). The effect of correlation and/or size of basis set should be clearly visible from the results. I tried to visit the URL given in the fourth reply, but could only get through to the parent page: http://fluid.nist.gov/ everything else seems to be unreachable for me?! Cheers, Ferenc Answers to the original posting: ---------------------------------------------------------------------- On Oct 9, 8:56am, CAVALLO@CHEMNA.DICHI.UNINA.IT wrote: > Subject: Re: CCL:halomethanes > > > dear ferenc, > > I tried to make some calculations on substituted haloalkanes, and I found > quite a strange behaviour indeed. > > I tried to optimize the geometry of the following molecules: > CF2Cl-CH3 and the corresponding anion CF2Cl-CH2(-). > Well, the parent molecule gave me any problem, while the anion simply > broke apart. The chlorine atom ran away like an anion and left the > CF2=CH2 alkene. I.E. I obtained the van der waals complex of > 1,1-difluoroethylene and chloride anion. More or less similar > results were obtained with similar molecules. > > I was using classical ab-initio without any correlation. The > basis set I used was 631G + 1 polar + 1 diffuse on all the atoms > (H included). Unhappy of this behaviour, I also tried the simple > mopac and I also tried DFT methods with NL corrections included. > (This last approach should include good correlation effects) but > the results were always the same. > > The only reference I could find on the subject is: > Bernardi et al. Gazz. Chim. Ital. 1990, 120, 301. > > I know that you were asking for cations and radicals instead > of anions, but I think that my experience could be of some > help in warning you with respect to strange behaviours in > haloalkanes. > > yours > luigi > > ------------------------------ > Dr. Luigi Cavallo > Dept. Of Chemistry > Univ. Of Naples > ITALY > Email cavallo@chemna.dichi.unina.it > ------------------------------ >-- End of excerpt from CAVALLO@CHEMNA.DICHI.UNINA.IT On Oct 9, 9:12am, Peter R. Schreiner wrote: > Subject: halomethanes > > > I would like to calculate the optimized structures and > > normal modes for a set of related compounds (halomethanes). > > > > Cl2-C-F2 (Dichlorodifluoromethane) > > / \ > > Cl-C-F2* Cl2-C-F2+ > > (radical) (cation) > > / \ > > Cl-C-F2+ C-F2 > > (cation) (carbene) > > \ > > C-F > > > > What type of basis-set would you recommend, that > > treats all of these species in a balanced way? > > > > My idea was to use polarization and diffuse functions > > to catch the ionic or radical character of these species. > > > > I belive, that Hartree-Fock (HF) will do a poor job for some > > of these molecules and one has to include electron-correlation > > even during optimization! Do you think that it is sensible > > to start from a HF minimum structure and to reoptimze with MP2? > > > > Calculating normal modes with MP2 will be quite expensive > > in terms of CPU and disk usage! Any idea about the "precision" > > that can be expected from such a calculation? > > > Dear Ferenc, > > The best compromise is probably DFT, preferrably B3LYP with a flexible > basis set, say 6-311+G* for geometry optimizations. For energies, > you will need a better basis for very accurate results. Others and > my experience would favor correlation-consistent basis sets of > triple zeta quality (e.g., cc-pVTZ) or higher, if you can afford it. > Ideally, you'd used CCSD(T) for the single points, but this may be too > expensive. Thus, the B3LYP/cc-pVTZ//B3LYP/6-311+G* + ZPVE should > be an acceptable compromise. > > For a mini-review on the performance of various methods with carbenes > see: J. Org. Chem. 1996, 61, 7030. > > Hope this helps, > Peter > > > -- > Dr. Peter R. Schreiner Computer-Chemie-Centrum > prs@organik.uni-erlangen.de Universitaet Erlangen-Nuernberg > Phone: +49-(0)9131-856533 Naegelsbachstr. 25 > FAX: +49-(0)9131-856566 D-91052 Erlangen, Germany > > NOTE: NEW ADDRESS from November 1, 1996: > > Institut fuer Organische Chemie > Universitaet Goettingen > Tammannstr. 2 Phone: +49-(0)551-393291 > D-37077 Goettingen, Germany FAX: +49-(0)551-399475 > > http://www.ccc.uni-erlangen.de/ecc/private > -- > Dr. Peter R. Schreiner Computer-Chemie-Centrum > prs@organik.uni-erlangen.de Universitaet Erlangen-Nuernberg > Phone: +49-(0)9131-856533 Naegelsbachstr. 25 > FAX: +49-(0)9131-856566 D-91052 Erlangen, Germany > > NOTE: NEW ADDRESS from November 1, 1996: > > Institut fuer Organische Chemie > Universitaet Goettingen > Tammannstr. 2 Phone: +49-(0)551-393291 > D-37077 Goettingen, Germany FAX: +49-(0)551-399475 > > http://www.ccc.uni-erlangen.de/ecc/private >-- End of excerpt from Peter R. Schreiner On Oct 9, 10:21am, E. Lewars wrote: > Subject: HALOMETHANES > Hello, some useful refs are: > 1. Theoretical Enthalpies of Formation of CHmCln > : Neutral Molecules and Cations > C. F. Rodrigues, D. K. Bohme, A. C. Hopkinson > J Phys Chem 1996, _100_ 2942-2949 > 2. Photochemical Isomerization of Dichloromethane in Argon Matrices > J Am Chem Soc 1990, _112_ 5117-5122. > Other papers by Hopkinson, in JPC and JACS, in the last 10 years, may also > be helpful. > Good Luck > ==== > Errol Lewars > === >-- End of excerpt from E. Lewars On Oct 9, 12:09pm, Russ Johnson wrote: > Subject: halomethane structures > Dear Ferenc, > First , there is some information on structures of fluoro methanes > and radicals at: > http://fluid.nist.gov/~drb/cgi/SpeciesData.html > > I would recommend a density functional method, as I've found it usually > gives very good geometries and frequencies for radicals and cations. Large > basis sets are usually not necessary so that B3LYP/6-31G* should > do quite well. > > You may have trouble with Cl2-C-F2+ , as both CF4+ and CCl4+ have non- > classical structures, they are more loosely bound complexes such as > CF3+ --- F. > > Good luck, > Russ > > > > > Russell D. Johnson III > Research Chemist > Physical and Chemical Properties Division > National Institute of Standards and Technology > Gaithersburg, MD 20899 > voice 301+975-2513 fax 301+975-3670 > email: russell.johnson@nist.gov >-- End of excerpt from Russ Johnson Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): Ferenc.Molnar@chemie.uni-regensburg.de --------------------------------------------------------------------------- Those who do not archive the past are condemned to retype it! -- Garfinkel & Spafford, Practical Unix Security --------------------------------------------------------------------------- From genghis@darkwing.uoregon.edu Mon Oct 14 10:15:14 1996 Received: from darkwing.uoregon.edu for genghis@darkwing.uoregon.edu by www.ccl.net (8.8.0/950822.1) id KAA22953; Mon, 14 Oct 1996 10:04:39 -0400 (EDT) Received: (from genghis@localhost) by darkwing.uoregon.edu (8.7.6/8.7.3) id HAA14711; Mon, 14 Oct 1996 07:04:37 -0700 (PDT) Date: Mon, 14 Oct 1996 07:04:37 -0700 (PDT) From: Dale Braden To: cclpost Subject: Summary: ab initio questions Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, Below are two questions I posted recently, followed by the responses. Thanks to all who responded. 1) The output of a frequency calculation normally includes the mass-weighted nuclear displacements for each normal mode, along with the reduced mass. Does anyone know how to calculate the *absolute* nuclear displacements, given the kind of data available from a frequency calculation by, for example, Gaussian 94? 2) In looking through the literature on calculations for organometallic complexes, I have noticed that polarization functions are often NOT added to the basis set for the transition metal, although they are always added to first-row atoms. Furthermore, for anionic systems, diffuse functions will be added only to the basis set used for the ligand atoms, but not to that for the metal. Now, perhaps calculations using such basis sets will agree well with experiment, but wouldn't this be fortuitous, since the basis set is unbalanced? Do the readers agree with the above practice? ---------------------- From hinsen@ibs.ibs.frMon Oct 14 06:55:54 1996 Date: Mon, 7 Oct 96 10:47:41 +0100 From: Konrad Hinsen You must divide each displacement by the square root of the mass of the respective atom. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-76.88.99.28 Institut de Biologie Structurale | Fax: +33-76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- ------------------ From irikura@leatherback.nist.govMon Oct 14 06:56:01 1996 Date: Mon, 07 Oct 1996 18:03:22 -0400 From: Karl Irikura I believe that the normal mode vectors reported by Gaussian are generated by (1) diagonalization of the standard mass-weighted hessian, (2) mass un-weighting the resulting orthonormal eigenvectors, (3) re-normalization of the pure displacement vectors. (I think the multiplier required for this normalization step is reported by Gaussian as the reduced mass.) These vectors are not orthogonal. If I recall properly, the ACES II program reports the straight mass-weighted, orthonormal eigenvectors and the GAMESS-US program reports the mass-unweighted (but not re-normalized) vectors. In my limited work (energetics) with organometallic compounds, I have found it important to include polarization functions on the central metal. I don't know the effects of diffuse functions because I've never done calculations on anionic metal systems. Best wishes, Karl Irikura ---------------------------------------------- Dr. Karl K. Irikura Physical and Chemical Properties Division National Institute of Standards and Technology Gaithersburg, MD 20899 voice: 301-975-2510 fax: 301-975-3670 e-mail: karl.irikura@nist.gov ---------------------------------------------- -------------------- From fredvc@esvax.dnet.dupont.comMon Oct 14 06:56:05 1996 Date: Mon, 7 Oct 96 22:49:07 EDT From: fredvc@esvax.dnet.dupont.com My exerience has been that programs are not consistent in what they print as the PED. One expects the coefficients of the mass-weighted displace- ments, i.e, "C" for C * sqrt(m) * q One program I used printed "C" values, another printed "C * sqrt(m)" values. What I do with a new program is run something where the it will clear what is printed, say, HF. From this I can tell what the authors of the code decided to print. I know, I know,... it should always be "C", but I find it best to test eahc code that I run. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com -------------------------------------------------------------------------------- Opinions expressed in this electronic message should ***> NOT <*** be taken to represent the official position(s) of the DuPont Company. *****> ANY OPINIONS EXPRESSED ARE THE PERSONAL VIEWS OF THE AUTHOR ONLY. <***** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -------------------- From hommes@organik.uni-erlangen.deMon Oct 14 06:56:10 1996 Date: Tue, 8 Oct 1996 21:26:28 +0100 (MET) From: Nico van Eikema Hommes Reply to: hommes@derioc1.organik.uni-erlangen.de > 1) The output of a frequency calculation normally includes the > mass-weighted nuclear displacements for each normal mode, along with the > reduced mass. Does anyone know how to calculate the *absolute* nuclear > displacements, given the kind of data available from a frequency > calculation by, for example, Gaussian 94? What you want, if I understand it correctly, is just a diagonalization of the second derivatives matrix. That should be no problem to do. If I remember correctly, both sets of displacements are available from a MOPAC run. > 2) In looking through the literature on calculations for organometallic > complexes, I have noticed that polarization functions are often NOT added > to the basis set for the transition metal, although they are always added > to first-row atoms. Furthermore, for anionic systems, diffuse functions > will be added only to the basis set used for the ligand atoms, but not to > that for the metal. Now, perhaps calculations using such basis sets will > agree well with experiment, but wouldn't this be fortuitous, since the > basis set is unbalanced? Do the readers agree with the above practice? The reason for this habit is practical: polarization for transition metals means adding f-functions. That makes the calculations much more expensive, many programs handle only spd basis sets, and popular codes like g94 can not compute first derivatives for the combination f-functions and ECPs. Yet it does indeed result in an unbalanced basis set and is not a good idea, despite all the literature "support" for it. Augmenting the metal basis set with diffuse functions is a different matter. These are important on electronegative elements, especially for the proper description of lone pairs (and not only for anionic systems), but play little role when added to the metal. In some cases, they may even worsen the result by leading to basis set superposition error, with the metal diffuse functions helping to describe ligand density. Hope this helps. Best wishes, Nico van Eikema Hommes -- Dr. N.J.R. van Eikema Hommes Computer-Chemie-Centrum hommes@ccc.uni-erlangen.de Universitaet Erlangen-Nuernberg Phone: +49-(0)9131-856532 Naegelsbachstr. 25 FAX: +49-(0)9131-856566 D-91052 Erlangen, Germany *************************************************************** Dale Braden Department of Chemistry University of Oregon Eugene, OR 97402 genghis@darkwing.uoregon.edu From mikha001@maroon.tc.umn.edu Mon Oct 14 11:14:51 1996 Received: from mhub2.tc.umn.edu for mikha001@maroon.tc.umn.edu by www.ccl.net (8.8.0/950822.1) id LAA23572; Mon, 14 Oct 1996 11:06:15 -0400 (EDT) Received: from maroon.tc.umn.edu by mhub2.tc.umn.edu; Mon, 14 Oct 96 10:06:15 -0500 Received: by maroon.tc.umn.edu; Mon, 14 Oct 96 10:06:15 -0500 Date: Mon, 14 Oct 1996 10:06:14 -0500 (CDT) From: Dmitri V Mikhailov To: chemistry@www.ccl.net Subject: summary for docking strategy Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, About 10 days ago I posted question about docking strategy. Thanks for everyone who replied. This information was really helpful. My original question and answers are shown below. Regards, Dmitri Mikhailov Ph.D. student ***************************************************** Univ. of Minnesota Medical School Department of Biochemistry Box 609, 420 Delaware St. SE Minneapolis MN 55455 tel. (612) 624-7107 fax. (612) 626-2325 e-mail: mikha001@maroon.tc.umn.edu ***************************************************** >Greetings everyone, >We are trying to do docking analysis for a system composed of a >negatively charged ligand and a basic protein. We are using the >Affinity module from MSI which allows flexible docking. >Could someone please point out reference(s) on general strategies >how to incorporate explicit solvent molecules in such a system and >analyze binding energies for different ligand conformations. >Thank you. >Regards, > >Dmitri Mikhailov >Ph.D. student ************************************************** From p.grootenhuis@organon.akzonobel.nlMon Oct 14 09:46:59 1996 Date: Fri, 4 Oct 1996 09:09:28 +0100 (WDT) From: Peter Grootenhuis To: Dmitri V Mikhailov Subject: docking Dear Dmitri, Check out our paper on docking negatively charged heparin derivatives on positively charged antithrombin III: JACS 1991, 113, 2743-2747. A better job should be possible since computers are a lot fasternow. Please send me the answers you get ... Thanks, Peter ______________________________________________________________________________ Prof. Dr. Peter D.J. Grootenhuis | N.V. Organon / CMC Dept. RK2337 | Phone : +31-412-661920 P.O. Box 20 / 5340 BH Oss | Fax : +31-412-662539 The Netherlands | E-mail : p.grootenhuis@organon.akzonobel.nl _________________________________|____________________________________________ ************************************************** From maxwelds@carbon.dmpc.comMon Oct 14 09:47:17 1996 Date: Fri, 4 Oct 1996 09:42:34 -0400 From: David Maxwell To: Dmitri V Mikhailov Subject: Re: CCL:docking strategy To be honest, I don't think that the version of Affinity that you have is quite ready for prime time use. I know this because I have been involved in improving the interface and working a little with the underlying code We have been in contact with MSI about improvements and hope that future versions will be better suited for docking. "Affinity" is somewhat misnamed as it is rather far from doing such calculations. In terms of explicit solvent molecules are you interested in adding them in the MSI calculations or are you looking for some other program which does docking with explicit solvent? If you are looking into calculating binding free energies (with explicit solvent) I can suggest a program that I did some testing on back at Yale. It is called MCPRO and is an extension of the BOSS program which handles proteins. I don't know what the current state is, but it has been used successfully in a number of cases. I did some testing on the sulfate binding protein and learned quite a bit in the process. If you want more information please contact Prof. William Jorgensen via e-mail, bill@adrik.chem.yale.edu. Good luck! -Dave ====================================================== Mail address: Dr. David Maxwell DuPont-Merck Pharmaceutical Company Experimental Station E500-3206A P.O. Box 80500 Wilmington, DE 19880-0500 Internet address: maxwelds@carbon.dmpc.com ====================================================== ************************************************ From wasserzr@llaxp.dnet.dupont.comMon Oct 14 09:47:46 1996 Date: Fri, 4 Oct 96 17:11:00 EDT From: wasserzr@llaxp.dnet.dupont.com To: Dmitri V Mikhailov Subject: Docking Strategy question This is in response to your question of analyzing binding energies for different ligand conformations. I have been using a different implementation of the method of Affinity in studies of binding of negatively charged ligands to metalloproteases. My initial endeavors are documented in "Fitting an Inhibitor Into the Active Site of Thermolysin: A Molecular Dynamics Case Study", Zelda R. Wasserman and C. Nicholas Hodge, PROTEINS: Structure, Function and Genetics, 24:227-237 (1996). In short I find that the final total energy of the system, averaged over a short time span of a few picoseconds, correlates well with agreement with crystal structure conformation, when such a conformation is known. In addition, I find the "true" conformation is found in a small but significant fraction of the simulations. Cluster analysis of the final conformations of a set of runs indicates this to be the major cluster formed in just about every case I have looked at. I have not attempted to calculate or compare binding energies of different ligands as I was dubious as to the validity of results. Work done here by my colleagues has shown those doubts to have been valid. I have limited experience with explicit solvation and the Affinity method. The work of others indicates that addition of a few water molecules may or may not improve the calculation. Full solvation is possible but computationally demanding and we have no experience in this area. Zelda R. Wasserman Principal Research Scientist The Dupont Merck Pharmaceutical Company Wilmington, DE 19880-0500 From iguana@one.net Mon Oct 14 23:14:49 1996 Received: from one.net for iguana@one.net by www.ccl.net (8.8.0/950822.1) id WAA08096; Mon, 14 Oct 1996 22:20:35 -0400 (EDT) Received: from iguana (port-12-26.access.one.net [206.112.194.126]) by one.net (8.7.5/8.7.5) with SMTP id WAA31561 for ; Mon, 14 Oct 1996 22:20:31 -0400 Date: Mon, 14 Oct 1996 22:20:31 -0400 Message-Id: <199610150220.WAA31561@one.net> X-Sender: iguana@mail.one.net X-Mailer: Windows Eudora Version 2.0.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: iguana@one.net (Ray Crawford) Subject: ab initio bond minimizations Howdy all -- I have a rather unique problem. I have a structure which was resolved from an electron density map. I wanted to compare this structure to another but when I went to do so using ab initio methods, I found that the single point energy of this molecule was horrendously large and any attempts to do energetic geometry minimizations led to different structures (changed torsions and bond angles). Further investigation led me to the conclusion that the main problem is that the errors in bond lengths (as small as they were) were drowning out the effects which I wanted to see the energetic changes for (torsional and angular changes). I recently saw a paper about a topic similar to this (I think it was in the Journal of Computational Chemistry)... If anyone has any references to work in this area or any ideas about how I can go about comparing these structures, I would appreciate it if you passed it on... All information will be promptly summarized and resubmitted... Thanks, Ray Crawford "Absence of proof is not proof of absence..." iguana@one.net -Richard Levine http://w3.one.net/~iguana The Lost World Micheal Crichton