From reichertd %-% at %-% mirlink.wustl.edu Sat Aug 23 17:19:33 1997 Received: from wugate.wustl.edu for reichertd()at()mirlink.wustl.edu by www.ccl.net (8.8.3/950822.1) id QAA12801; Sat, 23 Aug 1997 16:44:25 -0400 (EDT) Received: from mirlink.wustl.edu (mirlink.wustl.edu [128.252.155.1]) by wugate.wustl.edu (8.8.5/8.8.5) with SMTP id PAA13263; Sat, 23 Aug 1997 15:44:21 -0500 (CDT) Message-ID: Date: 23 Aug 1997 15:41:20 -0500 From: "David Reichert" Return-Receipt-To: "David Reichert" Subject: Summary Parameterization Tools To: "CCL post" , "Valentin Ananikov" X-Mailer: Mail*Link SMTP-MS 3.0.2 ************************************************ * David E. Reichert, Ph.D. * * Mallinckrodt Inst. of Radiology * * Div. Radiological Sciences, * * Washington University School of Medicine * * 510 S. Kingshighway Blvd., Campus Box 8225 * * St. Louis, MO 63110 * * * * phone: (314)362-8461 * * fax: (314)362-9940 * * e-mail: reichertd-0at0-mirlink.wustl.edu * ************************************************ <<<<<< Attached TEXT file named "CCL Parameterization Tools" follows >>>>>> Almost a month ago I posted a query: >From: David Reichert >Date: Tue, Jul 29, 1997 1:19 PM >Subject: CCL:Parameterization Tools >To: CCL post > >I'm looking for some info and/or code to help automate the development of >forcefield parameters, hopefully the list readers can provide some leads. >Given a set of x-ray or NMR structures and/or results from ab initio >calculations are there programs that can automate the development of >parameters for a given forcefield, ie eq bondlengths, angles, stretching >constants etc... Any pointers would be greatly appreciated. (I'm getting tired >of doing this by hand, there must be a better tool somewhere !) >thanks, >Dave The following is a summary of replies that I received. I'd like to thank everyone who took the time to send me some leads. -------------------------------------------------------------------------------------- From: dalke - at - mag.com Date: Tue, Jul 29, 1997 1:39 PM Subject: Re: CCL:Parameterization Tools To: David Reichert > Given a set of x-ray or NMR structures and/or results from ab initio > calculations are there programs that can automate the development of > parameters for a given forcefield, ie eq bondlengths, angles, stretching > constants etc X-PLOR can do this. See the man page at: http://xplor.csb.yale.edu/manual/htmlman/node56.html Andrew Dalke dalke %! at !% mag.com From: Richard Wisniewski Date: Tue, Jul 29, 1997 1:43 PM Subject: Re: CCL:Parameterization Tools To: David Reichert At your university the person to contact on this subject might be Dr Jay Ponder... Richard Wisniewski NASA ARC From: Dr. Mike Gilson Date: Tue, Jul 29, 1997 1:59 PM Subject: force field To: David Reichert Hi, I am not sure whether there is code to to this, but the following papers might conceivably be of interest.... good luck, Mike ==================================== author = "J. R. Maple and {M.-J.} Hwang and T. P. Stockfisch and U. Dinur and M. Waldman and C. S. Ewig and A. T. Hagler", title = "Derivation of Class {II} Force Fields. 1. {M}ethodology and Quantum Force Field for the Alkyl Functional Group and Alkane Molecules", OPTcrossref = "", OPTkey = "", journal = "J. Comput. Chem.", year = "1994", volume = "15", OPTnumber = "", pages = "162-182", OPTmonth = "", OPTnote = "", OPTannote = "" } -8 at 8- Article{cff2, author = "{M.-J.} Hwang and T. P. Stockfisch and A. T. Hagler", title = "Derivation of Class {II} Force Fields. 2. {D}erivation and Characterization of a Class {II} Force Field, {CFF}93, for the Alkyl Functional Group and Alkane Molecules.", OPTcrossref = "", OPTkey = "", journal = "J. Am. Chem. Soc.", year = "1994", volume = "116", OPTnumber = "", pages = "2515-2525", OPTmonth = "", OPTnote = "", OPTannote = "" } -: at :-Article{cff3, author = "J. R. Maple and {M.-J.} Hwang and T. P. Stockfisch and A. T. Hagler", title = "Derivation of Class {II} Force Fields. 3. {C}haracterization of a Quantum Force Field for Alkanes.", OPTcrossref = "", OPTkey = "", journal = "Isr. J. Chem.", year = "1994", volume = "34", OPTnumber = "", pages = "195-231", OPTmonth = "", OPTnote = "", OPTannote = "" } From: Andrew Rohl Date: Tue, Jul 29, 1997 6:45 PM Subject: Re: CCL:Parameterization Tools To: David Reichert Dr Julian Gale has a program GULP which can do this. His email is julian "at@at" ri.ac.uk Andrew From: Per-Ola Norrby Date: Wed, Jul 30, 1997 2:27 AM Subject: Re: CCL:Parameterization Tools To: David Reichert Dear David, I feel I must respond to your question. I do have such a tool, and I plan to give it away for free, but I must wait to have it accepted. I submitted it in May, so I hope to have some response soon. The reason I answer before I have something I can share is that what you requested is EXACTLY what I've been developing. There are some similar tools available already, but most are limited to one kind of data. I have made sure that I can include most kinds of experimental and theoretical results in the parameterization. I have been working with MacroModel, for those force fields my routines work without modification, but I've started to modify the routines for other packages that run under Unix. The main requirement is that you should be able to run the program from a Unix script, and generate a text output containing the force field predicted data. In short, what I do is predict bond lengths, angles, dihedrals, energies, cartesian energy derivatives etc. from the force field, compare it to the reference data, and automatically vary the parameters to obtain the best possible correspondance in a least squares sense. It's a bit tricky to find scale factors to allow the routines to treat all different kinds of data on an equal basis, but I have a working solution (which I continually modify). As for already existing tools, there are a few (I don't have experience with them, I've just read about them): * The BIOSYM PROBE program will allow you to optimize parameters to fit quantum chemical energies. It seems VERY efficient, and has been used successfully by both Hagler et al. (CFF), and Halgren et al. (MMFF). However, I believe you must be a member of the consortium to get access to it. See: A. T. Hagler et al., J. Comput. Chem., 15, 162 (1994). A. T. Hagler et al., J. Am. Chem. Soc., 116, 2515 (1994). T. A. Halgren, J. Am. Chem. Soc., 114, 7827 (1992). T. A. Halgren, J. Comput. Chem., 17, 490 (1996) and following papers in the same issue. * There are at least two programs I know about where you can define your own force field (including the functional form) and, I believe, automatically optimize the parameters. These are PEFF from Jan Dillen (J. L. M. Dillen, J. Comput. Chem., 13, 257 (1992)), and TINKER from Jay Ponder (http://dasher.wustl.edu/). There are several other published methods, but I'm not aware of any program that goes with them. Some are based on the original CFF by Lifson and Warshel, and there may be a program available from the Lyngby group (K. Rasmussen et al., Acta Chem. Scand., 48, 548 (1994) and following paper). I've started using my routines with TINKER and with MM3(94), it seems to work, but there are still a few bugs. Best Regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Research Associate * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon -AatT- medchem.dfh.dk, http://compchem.dfh.dk/ Message for David Reichert From: szilagyi : at : indy.mars.vein.hu Date: Wed, Jul 30, 1997 3:02 AM Subject: Re: CCL:Parameterization Tools To: David Reichert Dear David, we have developed a fully automatized parameterisation algorithm, which is going to be published in a couple of weeks. The method performs a statistical analyses of available structural sources and then an electronic sheet guided stepwise parameter adjustement is taken place. If you are interested in more details please let me know about your current research problem! Best wishes, -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Robert K. Szilagyi Mueller Laboratory ph.d. student Dept. Organic Chemistry University of Veszprem szilagyi-: at :-mm2.vein.hu Veszprem, H-8201 POB. 158; Egyetem u. 10. Phone: +36 88 422022 extn. 395 HUNGARY Mobile: +36 20 461413 Fax: +36 88 427492 http://mm1.vein.hu/ ====================================================================== ********** All opinions are my own, NOT my employer's ! ********** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From: szilagyi-0at0-indy.mars.vein.hu Date: Mon, Aug 4, 1997 1:03 AM Subject: Re: CCL:MM parameter development To: David Reichert Dear David, an automatic parameter optimisation tool was developed in our laboratory. We have tested on alkylphosphines (published in J.Mol.Struct. but not yet rolled out), alkylsilanes, ruthenium and tungsten organometallic complexes. It works fine and converges rapidly. The method will be published in J.Comput.Chem. very soon! The method developed can take into account any structural consideration based on X-ray, IR, Electron diffraction of microwave spectroscopy. If you are interested in more details let me know! Best wishes, -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Robert K. Szilagyi Mueller Laboratory ph.d. student Dept. Organic Chemistry University of Veszprem szilagyi -AatT- mm2.vein.hu Veszprem, H-8201 POB. 158; Egyetem u. 10. Phone: +36 88 422022 extn. 395 HUNGARY Mobile: +36 20 461413 Fax: +36 88 427492 http://mm1.vein.hu/ ====================================================================== ********** All opinions are my own, NOT my employer's ! ********** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From: Brian Teppen Date: Wed, Jul 30, 1997 12:50 PM Subject: CCL:Parameterization Tools -Reply To: David Reichert Hi, Dave: I have used a tool provided by Kjeld Rasmussen of the Technical University of Denmark, called CFF. He studied with Lifson way back around 1970 and has been developing Lifson's program as a parameter-fitting tool, rather than as a macromolecular simulator, as others have done. The program is a mix of Fortran for the actual nonlinear least-squares optimization and C for a graphical interface that allows one to monitor the progress of the parameter optimization. One can input molecular structures and molecular crystals, and one can optimize to structures, unit cell parameters, and vibrational frequencies simultaneously. So far, Dr. Rasmussen has given the source code to those who ask. He has an ftp server with a tar file that includes a user manual. You can contact him at kjr -x- at -x- kemi.dtu.dk Program descriptions and optimization examples can be found in: Engelsen, S. B.; Fabricius, J.; Rasmussen, K. Acta Chem. Scand. 1994, 48, 548-552; 553-565. Jonsdottir, S. O.; Rasmussen, K. New. J. Chem. 1995, 19, 1113-1122. Fabricius, J.; Engelsen, S. B.; Rasmussen, K. New. J. Chem. 1995, 19, 1123-1137. Niketic, S. R.; Rasmussen, K. The consistent force field: A documentation; Lecture Notes in Chemistry 3; Springer-Verlag: Heidelberg, FRG, 1977. Rasmussen, K.; Engelsen, S. B.; Fabricius, J.; Rasmussen, B. In Recent experimental and computational advances in molecular spectroscopy. NATO ASI Series C: Mathematical and Physical Sciences; Fausto, R., Ed.; Kluwer Academic Publishers: Dordrecht, 1993; Vol. 406, pp. 381-419. Best wishes, Brian J. Teppen teppen (- at -) srel.edu Advanced Analytical Center for Environmental Sciences Savannah River Ecology Laboratory University of Georgia Drawer E Aiken, SC 29802 phone:803-725-8157 fax:803-725-3309 Message for David Reichert From: Dayong He Date: Fri, Aug 1, 1997 1:46 PM Subject: Re: CCL:MM parameter development To: David Reichert Hi, David, Have you tried the scientists in MSI, there are several guys very expertise in developing force field. Dayong _____________________________________________________________________________ Dayong He Department of Chemistry Rutgers, The State University of New Jersey Piscataway, NJ 08855 Tel: (732)445-4619(o), Email: yong (- at -) rutchem.rutgers.edu _____________________________________________________________________________ Message for David Reichert From: Donald E. Williams Date: Tue, Aug 19, 1997 11:58 AM Intermolecular force field development with npg Program nbp (for nonbonded potentials) is a software tool which derives an optimized intermolecular force field from molecular crystal and/or molecular cluster data. The input to the program is a set of structures encoded in the mpa/mpg (for molecular packing analysis/molecular packing graphics) format. All atoms (or sites) in different molecules are assumed to interact via (exp-6-1) or (n-6-1) nonbonded potentials. Atoms of a given element can be classified into several potential types. The effect of net atomic (or site) charges is included in the force field. The force field can be scaled to one or more energies such as heats of sublimation or heats of association. The program can be used to find a customized force field for any training subset of structural and energy data, find a general force field for a large training set of data, or to extend an existing force field to include different types of atoms. The output from the program is an optimized intermolecular force field which best represents the training set data. Mpa/mpg is required for proper operation of nbp. A description of mpa/mpg is appended. Net atomic charges may be obtained with pdm97, which is also described. Brief history of our approach to intermolecular force field development Early efforts to produce intermolecular force fields began with graphite and noble gases. Crowell (1958) derived a C...C potential from graphite using the interlayer energy, interlayer distance, and compressibility. An analogous procedure was used by Williams (1972a) to find (exp-6) potentials for Ne, Ar, Kr, and Xe from crystal structure, heat of sublimation, and compressibility data. Kitaigorodsky's book (1961), "Organic Chemical Crystallography", stimulated a great deal of interest in the packing of organic molecules, especially hydrocarbons. He later published (1973) another treatise on the same subject. An early effort produced a quantitative nonbonded force field for aromatic hydrocarbon crystals (Williams, 1966). This paper was much cited and was designated a citation classic by the Institute for Scientific Information, publishers of the "Citation Index". The hydrocarbon work was extended to include nonaromatics (Williams, 1967) and net atomic charges (Williams, 1974). The overall method was described as "molecular packing analysis" (Williams, 1972b). The method for derivation of intermolecular force fields was further refined in connection with a study of perchlorohydrocarbon crystal structures (Hsu & Williams, 1980). Nonbonded potential functions were derived for nitrogen in azahydrocarbons (Williams & Cox, 1984), oxygen in oxohydrocarbons (Cox, Hsu, & Williams, 1981), fluorine in perfluorohydrocarbons (Williams & Houpt, 1986), chlorine in perchlorohydrocarbons (Hsu & Williams, 1980), and chlorine in dichlorine (Williams & Gao, 1997a). The current version of nbp was used to derive a force field for boron and hydrogen in crystalline boranes (Williams & Gao, 1997b). The number of workers and publications in this field has greatly expanded. There are now available a variety of intermolecular force fields from various research groups. Often the intermolecular force field was not the primary goal, but it was developed in connection with an intramolecular force field. Discussion and references to recent work can be found, for example, as articles in the series "Reviews in Computational Chemistry", in the Journal of Computational Chemistry, and other major journals. Proprietary force fields also have emerged where sometimes the basis for establishment of the parameters is not clearly stated. References Crowell, A. D.(1958). Potential Energy Functions for Graphite. J. Chem. Phys. 29, 446. Cox, S. R.; Hsu, L. Y.; Williams, D. E. (1981). Nonbonded Potential Function Models for Crystalline Oxohydrocarbons. Acta Cryst. A37, 293. Hsu, L. Y.; Williams, D. E. (1980). Intermolecular Potential Function Models for Crystalline Perchlorohydrocarbons. Acta Cryst. A36, 277. Kitaigorodsky, A. I. (1961). Organic Chemical Crystallography. Consultants Bureau, New York. Kitaigorodsky, A. I. (1973). Molecular Crystals and Molecules. Academic Press, New York. Williams, D. E. (1966). Nonbonded Potential Functions Derived from Crystalline Aromatic Hydrocarbons. J. Chem. Phys. 45, 3770. Williams, D. E. (1967). Nonbonded Potential Functions Derived from Crystalline Hydrocarbons. J. Chem. Phys. 47, 4680. Williams, D. E. (1972a). Direct Calculation of Thermal Expansion and Molecular Reorientation from Nonbonded Potential Anharmonicity and Thermal Amplitudes. Acta Cryst. A28, 84-88. Williams, D. E. (1972b). Molecular Packing Analysis. Acta Cryst. A28, 639-635 Williams, D. E. (1974). Coulombic Interactions in Crystalline Hydrocarbons. Acta Cryst. A30, 71. Williams, D. E.; Cox, S. R. (1984). Nonbonded Potentials for Aza- hydrocarbons. The Importance of the Coulombic Interaction. Acta Cryst. B40, 404. Williams, D. E.; Gao, D. (1997a). Effects of the Molecular Electric Potential and Anisotropic Repulsion in the Chlorine Dimer and Crystalline Chlorine. Inorg. Chem. 36, 782-786. Williams, D. E. & Gao, D. (1997b). Intermolecular Force Field Parameters for Boranes. Acta Cryst., Sec. B, submitted. Williams, D. E.; Houpt, D. J. (1986). Fluorine Nonbonded Potential Parameters Derived from Crystalline Perfluorocarbons. Acta Cryst. B42, 286. Williams, D. E.; Starr, T. L. (1977). Calculation of the Crystal Structures of Hydrocarbons by Molecular Packing Analysis. Comp. Chem. 1, 173. For further information contact: Dr. Donald E. Williams Department of Chemistry University of Louisville Louisville, KY 40292 USA email: dew01 (- at -) xray5.chem.louisville.edu Molecular Packing Analysis/Molecular Graphics Mpa/mpg is a suite of programs designed for molecular packing analysis and molecular packing graphics in the unix environment. The capability of the mpa module extends from minimization of the energy of association of two or more molecules (e.g., molecular clusters and host-substrate docking) to energy minimization of a molecular assembly in a crystal lattice of any space group symmetry (e.g., crystal polymorph prediction). The software is capable of predicting space groups and reduced cells in which a given molecule may crystallize. Provision for limited molecular flexibility is made through selected rotations about intramolecular bonds. Molecular and/or crystal symmetry restrictions may be selectively applied as desired. A library of commonly available intermolecular force fields is included (e.g., WH86, MM85, Biosym, Charmm, Dreiding, etc.), and provision is made for user supplied force fields. The program selects energy minimization by OREM (off-ridge eigenvector minimization), SD (steepest descents), or NR (Newton-Raphson) as appropriate for the model. All first and second derivatives of the energy are calculated analytically; the second derivative matrix (hessian) is diagonalized and its eigenvectors determined. Simulated annealing is included to aid in locating global, rather than subsidiary, energy minima. The molecular packing graphics (mpg) module is closely integrated with the molecular packing analysis module to give users fast, convenient, and useful graphical visualization of the results. To obtain an abstract of the program and a listing of example calculations, send an email request to dew01' at \`xray5.chem.louisville.edu. In summary, here are some principal capabilities of mpa/mpg: > minimization of nonbonded and hydrogen bonded energy in molecular clusters or crystals (includes molecular docking) > ab initio prediction of space group symmetry > uses (n-6-1) or (exp-6-1) interatomic potentials > built-in force field library (WH86, MM85, Biosym, CHARMM, etc.) > Newton-Raphson (NR), steepest descents (SD), and off-ridge eigenvector minimization (OREM) > OREM with simulated annealing (OREMWA) > provision for limited molecular flexibility > multiple molecules in asymmetric unit > accelerated convergence of lattice sums > convenient graphical visualization Also available: Pdm97, Least-Squares Fitting of the Molecular Electrostatic Potential With Net Atomic Charges and/or Multipoles Reliable net atomic charges/multipoles can be found by fitting the molecular electric potential with program pdm97. The program provides a choice of geodesic(1), Connolly(2), cubic(3), or user specified grid points for the electric potential. The program includes calculation of hyperbolic- restricted charge magnitudes(4). In addition to net atomic charges, the program also allows any combination of atomic dipoles/quadrupoles, bond dipoles, as well as the addition of lone pair electron sites if required. The program directly reads output files from Gaussian-92 and Gaussian-94 programs, and will accept edited input from any program which produces a molecular electric potential on a grid. Program pdm97 is the most complete and versatile software package available for this type of calculation. Molecular interactions occur during host-substrate docking, cluster, and crystal formation - whenever molecules associate with one another. The energy and geometry of molecular association is determined by the force field. As a component of the force field, an accurate set of net atomic charges is required. Or, if higher accuracy is needed, pdm97 can make extensions to the net atomic charge model in a variety of ways. A particularly useful feature of the program is the easy and transparent way in which fixed charges and charge dependency conditions are specified. By specifying appropriate charge dependencies (e.g., equal charges or equal sums of charges), chemical intuition can assist to produce charges which are transferable between related types of molecules or molecular ions. Hyperbolic-restricted charges are specifically designed to increase charge transferability. All charge calculation include a complete error treatment with standard deviations and correlations between variables. References (1) Spackman, M. A., "Potential Derived Charges Using a Geodesic Point Selection Scheme", J. Comput. Chem 1996, 17, 1-18 (2) Connolly, M. L., "Solvent-accessible Surfaces of Proteins and Nucleic Acids", Science 221, 709-713 (1983) (3) Williams, D. E., "Net Atomic Charge and Multipole Models for the Ab Initio Molecular Electric Potential", Rev. Comp. Chem. 1991, 2, 219-271. (4) Bayly, C. L.; Cieplak, P.; Cornell, W. D.; Kollman, P. A., "A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model", J. Phys. Chem. 1993, 97, 10269-10280. For further information contact Dr. Donald E. Williams, Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA. E-mail:dew01 ^at^ xray5.chem.louisville.edu Tel:(502)852-5975 Fax:(502)852-8149