Lawrence Berkeley National Laboratory Recent Work Title COMPUTER SIMULATION OF ORGANIC AND BIOLOGICAL MOLECULES. PROCEEDINGS OF THE WORKSHOP HELD AT ASILOMAR CONF. GROUNDS PACIFIC GROVE, CALIF., JAN. 5-8, 1981. Permalink https://escholarship.org/uc/item/97j907c0 Author Olson, A.J. Publication Date 1981 eScholarship.org Powered by the California Digital Library University of California RECEIVED LAWRENCE: LBL-12979<"'':a-. BERKELEY lABORATORY UC-48 . AUG 31 1981 CONF-810149 LIBRARY AND q(>CUMENTS SECTION NATIONAL RESOURCE FOR COMPUTATION IN CHEMISTRY COMPUTER SIMULATION OF ORGANIC AND BIOLOGICAL MOLECULES tA. ..s( Q) Q) ::::s'\ Q.. 9 Proceedings of the Workshop held at >- 0 0 Asilomar Conference Grounds 0... u 3 0 ~ ...... Pacific Grove, California u s:: :..... ...... --.0 , January S-8, 1981 z (::; <( \:S Q) 0 u~ 9 ,RCC Proceedi•.. ~ 1; ....J ,_:..... 0 :..... .. , January·l~.~~·;';. ~ u :..... L.U ::::s'\0 1":' L.U :......Q '· (::; Q) ~ :..... ..Q ..Q g a ,_ ::::s'\ 0 . 0' ....J (::; lA 0· :..... ~ (::; Q) s:: ~ E Q..- r- lA -- ..s::: (::; . -~ -~ ..s::: :....-5 l I , ~ ..s::: 0 Q) \ f . f 1 U...l- J .1 •. ~ . 1- 3 . i. ~ ~'---~:£~a~w~t'RENC~E·. BERKELEY lABORATORY f I ~ · ( UNIVERSITY OF G~LIFORNIA l( ~:~I .<':_..\ • ;,.· 1 .•. ~ ::' This work was supported by the Director, Office of Energy Research, Office of Basic Energy Sciences, Chemical Sciences Division of the U.S. Department of Energy under Contract No. W-7405-ENG-48 and under a grant from the National Science Foundation Grant No. CHE-7721305. '. DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor the Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or the Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof or the Regents of the University of California. LBL-12979 PROCEEDINGS of the workshop .~ .. COMPUTER SIMULATION OF ORGANIC AND BIOLOGICAL MOLECULES Sponsored by the NATIONAL RESOURCE FOR COMPUTATION IN CHEMISTRY Lawrence Berkeley Laboratory University of California Berkeley, California 94720 USA Held at Asilomar Conference Grounds Pacific Grove, California January 5-8, 1981 NRCC Proceedings No. 11 Edited by: Arthur J. Olson This work was supported by the Director, Office of Energy Research, Office of Basic Energy Sciences, Chemical Sciences Division of the U.S. Department of Energy under Contract No. W-7405-ENG-48 and by the ,.,.. National Science Foundation under Grant No. CHE-7721305. LBL-12979 PROCEEDINGS of the workshop COMPUTER SIMULATION OF ORGANIC AND BIOLOGICAL MOLECULES I Sponsored by the NATIONAL RESOURCE FOR COMPUTATION IN CHEMISTRY Lawrence Berkeley Laboratory University of California Berkeley, California 94720 USA Held at Asilomar Conference Grounds Pacific Grove, California January 5-8, 1981 NRCC Proceedings No. 11 Edited by: Arthur J. Olson This work was supported by the Director, Office of Energy Research, Office of Basic Energy Sciences, Chemical Sciences Division of the U.S. Department of Energy under Contract No. W-7405-ENG-48 and by the National Science Foundation under Grant No. CHE-7721305. '\ \ CONTENTS Workshop Participants .i v Foreword vi Introduction vii Session I Structures and Force Fjelds of Small Molecules: Molecular Mechanics, Pseudopotential, and Experimental Studies L. S. Bartell 1 Application of Consistent Force Field Techniques in the Area of Gas Phase \10:.- Molecular Structure Determination R.· L. Hilderbrandt 3 Applications of Steric Effects D. F. D.eTar 7 The Structures of Some Small Organic Molecules: Theory (ab-initio HF 3-21G) Versus Experiment (Neutron Diffraction at 20 K) G. A. Jeffrey 10 Session II Use of AMBER AND CHEM in Model Building Intermolecular Associations P. Kollman, P. Weiner, and A. Dearing 14 Computational Studies of Polynucleotide Flexibility W. K. Olson 19 Description and Application of the Molecular Structure Caltulator CHEMLAB A. J. Hopfinger 23 Session III Simulations of Protein Folding, Hydration and Interaction with Substrates H. A. Scheraga 27 Session IV Spectroscopic Calculations, Conformational Energy Minimization and Computer Graphics as Tools in Studying Protein Structure and Function B. Honig 31 Conformation and Dynamics of Biomolecules A. T. Hagler 35 Formation of Constrained Peptide Structures: Cyclic Peptides and Interchain Complexes G. Nemethy 40 _ Sjstematic Search in the Conformational Analysis of. Small.Molecules G. R. Marshall and R. A. Dammkoehler 46 Session V Modeling Statistics and Dynamics of a Protein Crystal J. Hermans 48 A Molecular Graphics and Energetics Study of Peptide Hydration · V. Madison 54 "··-. Session VI Some Recent Work in Molecular Mechanics N. L. A11 i nger 58 Session VII Water Structure in DNA Solutions and Conformatinal Transitions Induced by Solvent Effects E. Clementi 59 Preliminary Results on Convergence Acceleration in Monte-Carlo Computer Simulation on Water and Aqueous Solutions P. K, Mehrotra, M. Mezei, and D. L. Beveridge 63 iii WORKSHOP PARTICIPANTS Prof. Norman Allinger Prof. Anne Englert Department of Chemistry Chimie Generale University of Georgia Universite Libre de Bruxelles Athens, GA 30602 Avenue F.D. Roosevelt, 50" B-1050 Bruxelles Prof. Lawrence Bartell BELGIUM Department of Chemistry University of Michigan Prof. Arnold T•. Hagler · Ann Arbor, MI 48104 Department of Chemistry University of California at San Diego Prof. David L. Beveridge i''. :. La Jolla, CA · 92093 Chemistry Department Hunter College of the City University Prof. Jan Hermans of New York Department of Biochemistry 695 Park Avenue School of Medicine New York, NY 10021 University of North Carolina Chapel Hill, NC 27514 Dr. Stanley Burt Molecular Theory Laboratory Prdf. Richard L. Hilderbrandt Building lOOT Department of Chemistry SRI International North Dakota State University 333 Ravenswood Avenue Fargo, ND 58105 Stanford, CA 94025 Prof. Barry Honig Dr. Bruce Bush Department of Biophysics Merck and Company University of Illinois at Urbana-Champaign Building R 84-27 Urbana, IL 61801 Box 2000 Rahway, NJ 07065 Prof; Anton J. Hopfinger Department of Macromolecular Science Dr. Javid Case Case Institute of Technology Department of Chemistry Case Western Reserve University University of California University.Circle Davis, CA 95616 Cleveland, Ohio 44106 Dr. David Ceperley Prof. George Jeffrey NRCC Department of Crystallography Lawrence Berkeley Laboratory University of Pittsburgh Berkeley, CA 94720 Pittsburgh, PA 15260 Dr~ Enrico Clementi Dr. Robert Jernigan IBM NIH Department B-28, Building 703-1 Building 10, Room 4 B-56 P. 0. Box 390 Bethesda, MD 20205 Poughkeepsie, NY 12602 Prof. Peter Kollman Dr. Richard Cramer Department of Pharmaceutical Chemistry Smith, Kline and French Laboratories School of Pharmacy 1500 Spring Garden Street University of California P. 0. Box 7929 San Francisco, CA 94143 Philadelphia, PA 19101 Prof. I. D. Kuntz Dr. Georges Destree Department of Pharmaceutical Chemistry Centre des Calcul School of Pharmacy Universite Libre de Bruxelles University of California Avenue F.D. Roosevelt, 50 San Francisco, CA 94143 B-1050 Bruxelles ...· BELGIUM Prof. Robert Langridge Department of Pharmaceutical Chemistry Prof. Delos DeTar University of California Department of Chemistry San Francisco, CA 94143 Florida State University Tallahassee, FL 32306 Dr. William A. Lester, Jr. NRCC Lawrence Berkeley laboratory Berkeley, CA 94720 iv Prof. Gilda Loew Molecular Theory Laboratory Building lOOT SRI International 333 Ravenswood Avenue Stanford, CA 94025 Prof. Vincent Madison Department of Medicinal Chemistry University of Illinois at the Medical Center 833 South Wood Street Chicago, IL 60680 Prof. Garland Marshall Departments of Physiology .of Biophysics and of Computer Science Washington University 660 South Euclid Avenue St. Louis, MO 63110 Dr. George Nemethy Baker Laboratory of Chemistry Cornell University Ithaca, NY 14853 Dr. Arthur J. Olson NRCC Lawrence Berkeley Laboratory Berkeley, CA 94720 Prof. Wilma K. Olson Department of Chemistry Rutgers University/Busch Campus New Brunswick, NJ 08903 Dr. Gary Quigley Department of Biology, Room 16-743 Massachusetts Institute of Technology Cambridge, MA 02139 Dr. George Rose Department of Biological Chemistry Hershey Medical Center Pennsylvania State University Hershey, PA . 17033 Prof. H. A. Scheraga Baker Laboratory of Chemistry Cornell University Ithaca, NY 14853 Prof. Kent Wilson Department of Chemistry, B-014 University of California at San Diego La Jolla, CA 92093 v FOREWORD I The National Resource for Computation in Chemistry (NRCC) was established to make information on existing and developing computational methodologies available to all segments of the chemistry community, to make state-of-the-art computational facilities (hardware and software) accessible to the chemistry community,