Journal ArticleDOI
Development and testing of a general amber force field.
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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
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Journal ArticleDOI
Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles.
Christopher L. McClendon,Gregory D. Friedland,David L. Mobley,Homeira Amirkhani,Matthew P. Jacobson +4 more
TL;DR: A novel method, "MutInf", is presented, to identify statistically significant correlated motions from equilibrium molecular dynamics simulations, which should be a useful tool for finding novel or "orphan" allosteric sites in proteins of biological and therapeutic importance.
Journal ArticleDOI
Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field.
TL;DR: Important classes of compounds that performed suboptimally with OPLS_2005 show significant improvements and the results with popular small molecule force fields-OPLS_2005, GAFF, and CHARMm-MSI are compared.
Journal ArticleDOI
Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches
Huiyong Sun,Lili Duan,Fu Chen,Hui Liu,Zhe Wang,Peichen Pan,Feng Zhu,John Z. H. Zhang,John Z. H. Zhang,Tingjun Hou +9 more
TL;DR: The results show that the ff03 force field performs the best, but the predictions given by the tested force fields are comparable, implying that the MM/GBSA predictions are not very sensitive to force fields.
Journal ArticleDOI
AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA
Raviprasad Aduri,Brian T. Psciuk,Pirro Saro,Hariprakash Taniga,H. Bernhard Schlegel,John SantaLucia +5 more
TL;DR: Force field parameters for the 107 modified nucleotides currently known to be present in RNA are developed and will improve the functionality of AMBER so that simulations can now be readily performed on diverse RNAs having post-transcriptional modifications.
Journal ArticleDOI
Polymatic: a generalized simulated polymerization algorithm for amorphous polymers
TL;DR: In this article, a generalized structure generation methodology for amorphous polymers by a simulated polymerization technique and 21-step molecular dynamics equilibration is presented, which is particularly effective for high-Tg polymers.
References
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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.