From davis@nod.bms.com Fri Aug 2 06:57:32 1993 Date: 02 Aug 1993 10:57:32 -0400 From: davis@nod.bms.com (Malcolm Davis) Subject: Re: charges for charged To: CHEMISTRY@ccl.net Message-Id: <9308021457.AA04960@nod.bms.com> >>>>> Modesto Orozco writes: Modesto> Finally: If you use DP/semiempirical charges you Modesto> might scale the charges (see Merz's or our papers), Modesto> but ONLY if you deal with neutral molecules. If you Modesto> consider a charged molecules you must not scale the Modesto> charges. A possibility was to scale directly the MEP Modesto> and compute the charges for the ions from this scaled Modesto> MEP, whic h will mantein the total charge of the Modesto> molecule. In a paper which will appear in few months Modesto> in J.Comp.Aided Mol.Des., we demonstrate that the Modesto> scaling factor ab initioMEP/semiempiricalMEP is 1.00 Modesto> for cations and anions. That is you do not need to Modesto> scale anything when compute semiempirical charges for Modesto> cations and anions. Perhaps I am missing something, but since the classical electrostatic potential depends linearly upon the charges, the best fit to the scaled MEP is the set of scaled charges that are the best fit to the unscaled MEP, i.e., the charges that do not maintain the net charge of a charged molecule. So, I assume that the proposal is to do the fit with the net charge constrained. In this case, At any scaling S, you are trying to fit a potential which satisfies Gauss's law for an enclosed charge of S*Q with only a charge Q. So is it surprising that the best fits occur with S=1? In a state of confusion, Malcolm E. Davis USMail: Macromolecular Modeling Bristol-Myers Squibb P.O.Box 4000 Princeton, NJ 08530-4000 Email : davis@nod.bms.com Phone : 609-252-4324 FAX : 609-252-6030 Office: LV H.3812 From CUNDARIT@MSUVX1.MEMST.EDU Fri Aug 2 05:00:17 1993 Date: 02 Aug 1993 11:00:17 -0600 (CST) From: CUNDARIT@memstvx1.memst.edu Subject: Re: Ti parameters/basis sets To: rob@retina.chem.psu.edu Message-Id: <01H19MVBTH189AN4VV@MSUVX1.MEMST.EDU> hi, Our group has used the effective core potentials of Stevens et al. quite extensively, and we are most impressed with the results in terms of geometries and energetics. The Stevens scheme includes the outermost core in the "valence" space, so that for Ti this means that 10 electrons are replaced and the 3s and 3p are included explicitly. The various workers in the field have shown that the outer core are necessary for energetics of TM's when using ECPs. The Stevens scheme is nominally triple zeta for the valence (i.e., 4s, 4p and 3d). Another difference in the Steven's scheme is that the analytical form of the potentials themselves are derived in such a way so as to use as few gaussians as possible. Standard applications of this scheme are TR Cundari Organometallics 1993, 12, 1998. TR Cundari and MS Gordon JACS 1993, 115, 4210. TR Cundari JACS, 1992, 114, 10557. TR Cundari JACS, 1992, 114, 7879. So as not to make this an infomercial for just one ECP scheme, I should point out that other ECPs are available (e.g., the Hay-Wadt scheme and those derived by Pitzer, Ross, et al.) and have been used to good adavantage in computational TM chemistry; look at the work by Morokuma, Hay, Hall, etc. Tom From balbes@osiris.rti.org Mon Aug 2 08:27:17 1993 Date: Mon, 2 Aug 93 12:27:17 -0400 From: balbes@osiris.rti.org (Lisa Balbes) Message-Id: <9308021627.AA05602@osiris.rti.org> To: chemistry@ccl.net Subject: Solvation Summary I was pleasantly suprised by both the volume and quality of the responses to my request. Below is the abridged verion - just the paper references. Several people sent personal observation on the theory of solvation, and one person sent the complete reference list from his most recent paper. Anyone interested in the complete text of responses can email me directly at balbes@osiris.rti.org. Thanks again to everyone who replied! Lisa P.F.W. Stouten, C. Frommel, H. Nakamura & C. Sander, "An Effective Solvation Term Based on Atomic Occupancies for Use in Protein Simulations," Mol. Simulation 10 (1993) 97-120. A good review of quantum mechanical approaches to solvation is in J. Tomasi, R. Bonaccorsi, R. Cammi, F.J. Olivares del Valle Theoretical chemistry in solution. Some results and persepctives of the continuum methods and in particular of the polarizable continuum model J. Mol. Struct. (Theochem), 234, 401-424, 1991. For empirical (non-quantum) activity you might look at: B. Honig, K. Sharp, A.-S. Yang, Macroscopic models of aqueous solutions: Biological and chemical appications, J. Phys. Chem., 97, 1101-1109, 1993. overview of some different approaches: A. Warshel, Computer Modelling of Chemical Reactions in Enzymes and Solutions, John Wiley & Sons, New York, 1991 Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. W. L. Jorgensen {\it Acc. Chem. Res.}, {\bf 22}, 184 (l989). Computational Insights on Intermolecular Interactions and Binding in Solution. W. L. Jorgensen {\it Chemtracts - Organic Chemistry}, {\bf 4}, 91-119 (1991). The Importance of Secondary Interactions in Triply Hydrogen Bonded Complexes: Guanine-Cytosine vs. Uracil-2,4-Diaminopyridine. W. L. Jorgensen and J. Pranata {\it J. Am. Chem. Soc.},{\bf 112},2008 (1990). A Priori Evaluation of Aqueous Polarization Effects Through Monte Carlo QM-MM Simulations. Jiali Gao and Xinfu Xia {\it Science}, {\bf 258}, 631 (1992). Effects of Hydration on the Claisen Rearrangement of Allyl Vinyl Ether from Computer Simulations. Daniel L. Severance and William L. Jorgensen {\it J. Am. Chem. Soc.}, {\bf 114}, 10966 (1992). What follows are references from the laboratories of Arieh Warshel at U.S.C.: J. Comp. Chem. 14(2) 161 J. Biol. Chem. 267(36) 25625 J. Chem. Phys. 97(6) 4264 J. Chem. Phys. 97(5) 3100 J. Comp. Chem. 13(2) 199 J. Phys. Chem. 95(22) 8445 J. Chem. Phys. 95(6) 4366 J.A.C.S. 113(13) 4800 J. Phys. Chem. 94(1) 460 J. Chem. Phys. 91(6) 3647 semi-empirical MO level for small molecules C. J. Cramer and D. G. Truhlar, Journal of Computer-Aided Molecular Design, vol. 6, 629-666(1992) at the MM-MD level for bio- macromolecules J. Guenot and P. A. Kollman, Protein Science, vol. 1, 1173-1184 and 1185-1205(1992) W.F. von Gunsteren & H.J.C. Berendsen (1990) Angew. Chem., Int. Ed. Engl. 29, 922 R. A. Friedman and B. Honig (1992) "The Electrostatic Contribution to DNA Base-STacking Interactions" Biopol 32, 145-159 Free energy calculations in different solvents by Rao and Singh (JACS, 111, 3125, 1989; 112, 3803, 1990; and 113, 4381, 1991) describe solvation differences in aqueous and non-aqueous solvents. Reviews: ------- For Macroscopic models: Honig et. el. J. Phys. Chem., 97, 1101, 1993. For SCF models: Cramer and Truhlar, J. Comp-Aided Drug Design, 6, 629, 1992. "Molecular Modeling in Solvent", G.W.A. Milne, M.C. Nicklaus, M. Hodoscek, J. Mol. Struct. 291 (1993) 89-103. % This came directly from a computer and is not to be doubted or disbelieved. % Lisa Balbes Osiris Consultants balbes@osiris.rti.org 2229B Hedgerow Rd, Columbus, OH 43220 614-442-9850 FAX: 614-451-5860 From davis@nod.bms.com Fri Aug 2 13:57:48 1993 Received: from cliff.bms.com for davis@nod.bms.com by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA03659; Mon, 2 Aug 1993 17:59:33 -0400 Received: from nod.bms.com by cliff.bms.com (PMDF #2529 ) id <01H1A1SXJ5JK000JTT@cliff.bms.com>; Mon, 2 Aug 1993 18:00:09 EST Received: by nod.bms.com (920330.SGI/920502.SGI) for @cliff.bms.com:CHEMISTRY@ccl.net id AA01351; Mon, 2 Aug 93 17:57:48 -0400 Date: 02 Aug 1993 17:57:48 -0400 From: davis@nod.bms.com (Malcolm Davis) Subject: Re: charges for charged In-Reply-To: <9308021457.AA04960@nod.bms.com> (davis) To: CHEMISTRY@ccl.net Message-Id: <9308022157.AA01351@nod.bms.com> X-Envelope-To: CHEMISTRY@ccl.net Content-Transfer-Encoding: 7BIT Obviously :-) in my previous message "Re: charges for charged" Malcolm> the best fit to the scaled MEP is the set of scaled Malcolm> charges that are the best fit to the unscaled MEP should have been the best fit to the scaled MEP is the set of charges that best fit the unscaled MEP, scaled by the same factor With appologies for spreading my confusion, Malcolm E. Davis USMail: Macromolecular Modeling Bristol-Myers Squibb P.O.Box 4000 Princeton, NJ 08530-4000 Email : davis@nod.bms.com Phone : 609-252-4324 FAX : 609-252-6030 Office: LV H.3812 From raman@bioc01.uthscsa.edu Mon Aug 2 11:48:52 1993 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA03528; Mon, 2 Aug 1993 17:48:28 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Mon, 2 Aug 1993 16:48:57 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA08659; Mon, 2 Aug 93 16:48:53 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9308022148.AA08659@bioc01.uthscsa.edu> Subject: Re: DNA-protein interactions? To: bishop@lisboa.ks.uiuc.edu Date: Mon, 2 Aug 1993 16:48:52 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <9307302109.AA07334@lisboa.ks.uiuc.edu> from "Tom Connor Bishop" at Jul 30, 93 04:09:27 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1352 Tom The following citations might interest you: 1. There was a recent issue of CURRENT OPINION IN STRUCTURAL BIOLOGY dedicated to "Protein-Nucleic Acid Interactions". Vol. 3 (#1) [1993] Particularly the article entitled "Protein-NA interactions by NMR" by Bob Kaptein, which appears on p. 50 is quite interesting. 2. Kothekar, V FEBS Lett. 274, 217 (1990) Computer simuation of the Zinc finger motifs. 3. A paper from Andy McCammons's group on the "Possion-Boltzmann analysis of lambda represson-operator interactions" was published in Biophys. J. 63, 1280. Hope this helps! Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From raman@bioc01.uthscsa.edu Mon Aug 2 11:54:52 1993 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA03599; Mon, 2 Aug 1993 17:54:20 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Mon, 2 Aug 1993 16:54:58 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA08684; Mon, 2 Aug 93 16:54:53 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9308022154.AA08684@bioc01.uthscsa.edu> Subject: Re: GenBank? To: DAVID%UCONNVM.BITNET@phem3.acs.ohio-state.edu (Carl David) Date: Mon, 2 Aug 1993 16:54:52 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <01H15GN3VDC68WXTJ4@phem3.acs.ohio-state.edu> from "Carl David" at Jul 30, 93 11:02:22 am X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1857 Carl: The latest version of the EMBL data bank can be accessed very easily if you had a GOPHER client (I already posted this info. to this group a couple of months ago!). If you have a Gopher client running then do the following: gopher ftp.embl-heidelberg.de and follow the menu and retrieve the sequence of interest. you can also use the above address to FTP. The contents of this site are mirrored in "fly.bio.indiana.edu" and "merlot.welch.jhu.edu" which too are gopher sites. Cheers -raman > I need to access a primary protein structure which has been deposited in > the "GenBank/EMBL Data Bank" with accession number ... > Can someone help me locate this site (and presuambly its e-mail address) > so that I can access this data? > Thanks. > Carl David > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator > OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net > CHEMISTRY-SEARCH@ccl.net --- search the archives, read help.search file first > --- > > -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From d3f012@pellucidar.pnl.gov Mon Aug 2 08:01:28 1993 Received: from pnlg.pnl.gov for d3f012@pellucidar.pnl.gov by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA04250; Mon, 2 Aug 1993 18:47:07 -0400 Received: from pellucidar.pnl.gov (130.20.182.74) by pnlg.pnl.gov; Mon, 2 Aug 93 15:42 PDT Received: by pellucidar.pnl.gov (920330.SGI/920502.SGI) for @pnlg.pnl.gov:chemistry@ccl.net id AA23005; Mon, 2 Aug 93 15:01:28 -0700 Date: Mon, 2 Aug 93 15:01:28 -0700 From: d3f012@pellucidar.pnl.gov Subject: Water summary To: chemistry@ccl.net Message-Id: <9308022201.AA23005@pellucidar.pnl.gov> X-Envelope-To: chemistry@ccl.net Some time ago, I posted a question regarding Biosym's use of a flexible hybrid SPC/TIP3P water model. I've summarized, below, the unedited responses I received. Apparently, there is no journal reference for Biosym's model, but one appears to be in the works. After reading response #2, it's not clear to me what the original motivation for using the flexible SPC/TIP3P hybrid water model was in the first place. It does not appear that the answers are any better, and in fact somewhat worse in the rdf for O-O 2nd peak. Mark Thompson ####################################### Mark: We have done lots of tests on the biosym water model and find that it is probably neither a lot better nor a lot worse than other models. The discrepancies between it and other models had us worried at first, also. Unfortunately, we could not convince either JCP or JPC to publish an accounting of this model, so that others like you and us would not have to ask and answer the same questions. We are currently working on another manuscript with an extended description and comparison with other models that these journals might find more palatable. I'll check with my coworkers about sending you a preprint of the previous manuscript. Terry R. Stouch, Ph.D. Room H3812, Department of Macromolecular Modeling Bristol-Myers Squibb Pharmaceutical Research Institute P.O. Box 4000, Princeton, NJ 08543-4000 PH: (609)252-5442 - FAX: (609)252-6030 - EMAIL: Stouch@bms.com Telex: 4754082 BRMYSQ PRIN For UPS or FedEx: Rt. 206 and Provinceline Road, Lawrenceville, NJ 08648 T ####################################### Water Model in CVFF ------------------- This is in response to Mark Thompson's questions on the water model in CVFF used in Discover. CVFF water model uses the nonbond parameters (charge and VDW) of SPC water. However, it is flexible and has the internals of TIP3P. Howard Alper and Terry Stouch at Bristol-Meyers Squibb; Tom Thacher and I at Biosym Technologies have collaborated on the molecular dynamics simulation on liquid water to study its structure, thermodynamic and dynamic properties under different simulation conditions. In a nutshell, the simulation results indicate that this water model is a fairly reasonable one. The liquid structure compares well with experimental results. The first peak positions of O-O O-H H-H radial distribution functions and second peaks of O-H and H-H are all within 0.1 A of experimental values. The second peak of O-O is off by about 1.0 A. The intermolecular energy is within 0.2 kcal/mol (~ 2%) of experimental value. Equilibrium density is within 3% difference with the experimental value. Diffusion coefficient, however, does not agree so well and is off by more than a factor of 2 compared with experiment. This may however be due to the simulation conditions and we are investigating this also. We are in the process of documenting our results and further details will be provided there. Kit Lau Application Scientist Discover Group Biosym Technologies e-mail kit@biosym.com ######################################## d ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. ************************************************************************** From modesto@doctor.chem.yale.edu Mon Aug 2 15:59:09 1993 Received: from DOCTOR.CHEM.YALE.EDU for modesto@doctor.chem.yale.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA05277; Mon, 2 Aug 1993 20:07:06 -0400 Received: by doctor.chem.yale.edu; Mon, 2 Aug 93 19:59:09 EDT Date: Mon, 2 Aug 93 19:59:09 EDT From: Modesto Orozco Message-Id: <9308022359.AA06157@doctor.chem.yale.edu> To: CHEMISTRY@ccl.net Subject: Charges (II, and last) To M.E.Davis and any other guy in state of confusion. A lot of people is using semiempirical methods to obtain MEPs and then fit the ESP charges. The semiempirical ESP and ab initio charges correlate well and then it was suggested to use the slope of the regression line abinitio = c* semiemp as a scaling factor. The charges are determined at the smiempirical level (keepi ng the constrain that SUMQ=0.0) and after this are scaled, since SUMQ=0, SUMQsca l are 0 and the monopole is conserved (not the dipole of course). The point is that this scaling of charges is exactly equivalent to the direct scaling of the QM MEP (within the experimental error) for nuetral molecules. The n, do not worry, use the standard way to obtain scaled semiempirical charges. For charged molecules the history is different, if we repeat the process and get a regression between charges: abinitio = c * semiemp we will get almost sure ly a c different to 1. Unfortunately the "scaled" charges will not mantein the total monopole and the errors in the Classical MEP (the real important number) will be huge. The idea of the scaling is that we can modify "empirically" the semiempirical QM MEP to make it more similar to a higher level MEP, and then get a set of "semiempirical" charges which better reproduce the electrostatic characteristics of the molecule. That is all, just a trick!. Then, as a summary, if you wish to obtain charges, and you believe semiempirical methods can be good, I suggest: i) Take a beer ii) Compute the semiempirical QM/MEP iii) Fit the ESP charges manteining the total charge of the molecule. iv) If the molecule is charged that is all. v) If the molecule is neutral and you feel it is similar to those considered to determine the scaling factors in Merz's or our works, then scale the semiempirical charges by the factors reported in these papers. vi) Go to step 1? And remember, before using a semiempirical method to get charges be sure that it is suitable to represent your molecule. Best - Modesto -