Journal ArticleDOI
Development and testing of a general amber force field.
Reads0
Chats0
TLDR
A general Amber force field for organic molecules is described, designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens.Abstract:
We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 A, which is comparable to that of the Tripos 5.2 force field (0.25 A) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 A, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 A and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching.read more
Citations
More filters
Journal ArticleDOI
CHARMMing: A new, flexible, web portal for CHARMM
Benjamin T. Miller,Rishi P. Singh,Jeffery B. Klauda,Milan Hodošček,Bernard R. Brooks,H. Lee Woodcock +5 more
TL;DR: A new web portal for the CHARMM macromolecular modeling package, CHARMMing (CHARMM interface and graphics, http://www.charmming.org), is presented, which provides a user-friendly interface for the preparation, submission, monitoring, and visualization of molecular simulations.
Journal ArticleDOI
Quantum chemical accuracy from density functional approximations via machine learning.
Mihail Bogojeski,Leslie Vogt-Maranto,Mark E. Tuckerman,Mark E. Tuckerman,Klaus-Robert Müller,Klaus-Robert Müller,Klaus-Robert Müller,Kieron Burke +7 more
TL;DR: In this paper, the authors leverage machine learning to calculate coupled-cluster energies from DFT densities, reaching quantum chemical accuracy (errors below 1 kcal/mol-1) on test data.
Journal ArticleDOI
Supramolecular assembly promotes the electrocatalytic reduction of carbon dioxide by Re(I) bipyridine catalysts at a lower overpotential.
Charles W. Machan,Steven A. Chabolla,Jian Yin,Michael K. Gilson,F. Akif Tezcan,Clifford P. Kubiak +5 more
TL;DR: Electrochemical studies, spectroelectrochemical measurements, and molecular dynamics simulations indicate that these methyl acetamidomethyl groups promote the formation of a hydrogen-bonded dimer, demonstrating that noncovalent self-assembly can modulate the catalytic properties of metal complexes by favoring alternate catalytic pathways.
Journal ArticleDOI
5-N-methylated quindoline derivatives as telomeric g-quadruplex stabilizing ligands: effects of 5-N positive charge on quadruplex binding affinity and cell proliferation.
Yu Jing Lu,Tian Miao Ou,Jia Heng Tan,Jin-Qiang Hou,Wei Yan Shao,Dan Peng,Ning Sun,Xiaodong Wang,Wei Bin Wu,Xian Zhang Bu,Zhi Shu Huang,Dik-Lung Ma,Kwok Yin Wong,Lian Quan Gu +13 more
TL;DR: A series of 5-N-methyl quindoline (cryptolepine) derivatives as telomeric quadruplex ligands was synthesized and evaluated, showing a remarkable cessation in population growth and cellular senescence phenotype and accompanied by a shortening of the telomere length.
Journal ArticleDOI
An improved method to predict the entropy term with the MM/PBSA approach
Jacob Kongsted,Ulf Ryde +1 more
TL;DR: A method is suggested to calculate improved entropies within the MM/PBSA approach (molecular mechanics combined with Poisson–Boltzmann and surface area calculations) to estimate protein–ligand binding affinities, and it is shown that it gives more stable results and often improved predictions of the relative binding Affinities.
References
More filters
Journal ArticleDOI
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Wendy D. Cornell,Piotr Cieplak,Piotr Cieplak,Christopher I. Bayly,Christopher I. Bayly,Ian R. Gould,Ian R. Gould,Kenneth M. Merz,Kenneth M. Merz,David M. Ferguson,David M. Ferguson,David C. Spellmeyer,David C. Spellmeyer,Thomas R. Fox,James W. Caldwell,Peter A. Kollman +15 more
TL;DR: Weiner et al. as mentioned in this paper derived a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases.
Journal ArticleDOI
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
TL;DR: In this paper, the authors present an approach to generate electrostatic potential (ESP) derived charges for molecules, which optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule.
Journal ArticleDOI
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
TL;DR: The first published version of the Merck molecular force field (MMFF) is MMFF94 as mentioned in this paper, which is based on the OPLS force field and has been applied to condensed-phase processes.
Journal ArticleDOI
A new force field for molecular mechanical simulation of nucleic acids and proteins
S. J. Weiner,Peter A. Kollman,David A. Case,U. C. Singh,Caterina Ghio,Giuliano Alagona,Salvatore Profeta,Paul K. Weiner +7 more
TL;DR: In this paper, a force field for simulation of nucleic acids and proteins is presented, which is based on the ECEPP, UNECEPP, and EPEN energy refinement software.
Journal ArticleDOI
How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules
TL;DR: In this paper, the authors present conformational energies for a molecular mechanical model (Parm99) developed for organic and biological molecules using the restrained electrostatic potential (RESP) approach to derive the partial charges.