Joshua Buckner, Xiaorong Liu, Arghya Chakravorty, Yujin Wu, Luis F. Cervantes, Thanh T. Lai, Charles L. Brooks,
CHARMM is rich in methodology and functionality as one of the first programs addressing problems of molecular ... molecule ligands. When combined with the highly developed CHARMM parameters for proteins, nucleic acids, small molecules, lipids, ... other biologically relevant building blocks, and the versatile CHARMM scripting language, CHARMM has been a trendsetting platform for modeling studies ... further enhance the utility of accessing and using CHARMM functionality in increasingly complex workflows associated with modeling ...
Tópico(s): Mass Spectrometry Techniques and Applications
2023 - American Chemical Society | Journal of Chemical Theory and Computation
Seonghoon Kim, Jumin Lee, Sunhwan Jo, Charles L. Brooks, Hui Sun Lee, Wonpil Im,
... problem, we have developed Ligand Reader & Modeler in CHARMM-GUI. Users can upload ligand structure information in ... files by searching for the ligand in the CHARMM force field library or using the CHARMM general force field (CGenFF). In addition, users can ... Ligand Reader & Modeler can be used in other CHARMM-GUI modules to build a protein-ligand simulation system for all supported simulation programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Ligand Reader & Modeler is available as a ...
Tópico(s): Enzyme Structure and Function
2017 - Wiley | Journal of Computational Chemistry
Sunhwan Jo, Xi Cheng, Jumin Lee, Seonghoon Kim, Sang‐Jun Park, Dhilon S. Patel, Andrew H. Beaven, Kyu Il Lee, Huan Rui, Soohyung Park, Hui Sun Lee, Benoı̂t Roux, Alexander D. MacKerell, Jeffrey B. Klauda, Yifei Qi, Wonpil Im,
CHARMM‐GUI, http://www.charmm-gui.org , is a web‐based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM‐GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM‐GUI has been widely adopted for various purposes ... Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have ...
Tópico(s): RNA and protein synthesis mechanisms
2016 - Wiley | Journal of Computational Chemistry
Qiang Cui, Marcus Elstner, Efthimios Kaxiras, Thomas Frauenheim, Martin Karplus,
... SCC-DFTB) method, has been implemented in the CHARMM program and tested on a number of systems ... presence of the enzyme, the overall SCC-DFTB/CHARMM results are in somewhat worse agreement with the B3LYP/6-31+G(d,p)/CHARMM values; the rms error in the energies is 5.4 kcal/mol. Single-point B3LYP/CHARMM energies at the SCC-DFTB/CHARMM optimized structures were found to be very similar to the full B3LYP/CHARMM values. The relative stabilities of the αR and ... dynamics simulations in vacuum and in solution. Although CHARMM and SCC-DFTB give qualitative different results in ...
Tópico(s): Erythrocyte Function and Pathophysiology
2000 - American Chemical Society | The Journal of Physical Chemistry B
Irena Roterman, M.H. Lambert, K. D. Gibson, Harold A. Scheraga,
... N′-methyl amide have been computed using the CHARMM potential, the all-atom AMBER potential, and the ... before and after adiabatic relaxation. Maps using the CHARMM and AMBER potentials were determined with values of ... was carried out using flexible geometry for the CHARMM and AMBER potentials, and using rigid geometry for ... region (φ −70°, ψ ∼ 70°). The maps with CHARMM and AMBER with ε = 4.0 and with ... adiabatic relaxation with flexible geometry, the maps with CHARMM and AMBER became very similar; the lowest energies ...
Tópico(s): Protein Structure and Dynamics
1989 - Taylor & Francis | Journal of Biomolecular Structure and Dynamics
Sunhwan Jo, Taehoon Kim, Vidyashankara Iyer, Wonpil Im,
CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a ... usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to ... we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together ...
Tópico(s): Mass Spectrometry Techniques and Applications
2008 - Wiley | Journal of Computational Chemistry
... widely. Furthermore, some include all atoms (AMBER and CHARMM PARAM22), whereas others are extended-atom models that ... polar hydrogens able to form hydrogen bonds explicitly (CHARMM PARAM19 and GROMOS). How these differences affect the ... D. States D.J. Swaminathan S. Karplus M. CHARMM: a program for macromolecular energy minimization and dynamics ... 1995; 117: 5179-5197Crossref Scopus (10933) Google Scholar), CHARMM PARAM19 (Brooks et al., 1983Brooks B.R. Bruccoleri ... D. States D.J. Swaminathan S. Karplus M. CHARMM: a program for macromolecular energy minimization and dynamics ...
Tópico(s): Nanopore and Nanochannel Transport Studies
2002 - Elsevier BV | Biophysical Journal
Abhishek A. Kognole, Jumin Lee, Sang‐Jun Park, Sunhwan Jo, Payal Chatterjee, Justin A. Lemkul, Jing Huang, Alexander D. MacKerell, Wonpil Im,
... oscillator model, Drude Prepper has been developed in CHARMM‐GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre‐equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular ... FF‐based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude ... The capabilities and availability of Drude Prepper in CHARMM‐GUI is anticipated to greatly facilitate the application ...
Tópico(s): Spectroscopy and Quantum Chemical Studies
2021 - Wiley | Journal of Computational Chemistry
Kenno Vanommeslaeghe, Elizabeth Hatcher, Chitrangada Acharya, Subhas C. Kundu, Shan Zhong, J. Shim, Eva Darian, Olgun Guvench, Pedro E. M. Lopes, Igor Vorobyov, Alexander D. MacKerell,
Abstract The widely used CHARMM additive all‐atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug‐like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range ... CGenFF thus makes it possible to perform “all‐CHARMM” simulations on drug‐target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems. © 2009 Wiley ...
Tópico(s): Lipid Membrane Structure and Behavior
2009 - Wiley | Journal of Computational Chemistry
Dingguo Xu, Daiqian Xie, Hua Guo,
... region in our simulations was characterized by the CHARMM all atom force field (24MacKerell Jr., A.D. ... 118, as well as the biapenem substrate. The CHARMM van der Waals parameters were used for the ... All calculations reported here were carried out using CHARMM (26Brooks B.R. Bruccoleri R.E. Olafson B. ... 7260-7268Crossref Scopus (3322) Google Scholar) implemented in CHARMM (28Cui Q. Elstner M. Kaxiras E. Frauenheim T. ... results, we have also performed single point B3LYP/CHARMM calculations along the semiempirical reaction path. The large ...
Tópico(s): Drug Transport and Resistance Mechanisms
2006 - Elsevier BV | Journal of Biological Chemistry
Wonmuk Hwang, Steven L. Austin, Arnaud Blondel, Eric D. Boittier, Stefan Boresch, Matthias Buck, Joshua Buckner, Amedeo Caflisch, Hao-Ting Chang, Xi Cheng, Yeol Kyo Choi, Jhih‐Wei Chu, Michael F. Crowley, Qiang Cui, A. Damjanović, Yuqing Deng, M. Devereux, Xinqiang Ding, Michael Feig, Jiali Gao, David R. Glowacki, James E. Gonzales, Mehdi Bagheri Hamaneh, Edward Harder, Ryan L. Hayes, Jing Huang, Yandong Huang, Phillip S. Hudson, Wonpil Im, Shahidul M. Islam, Wei Jiang, Michael R. Jones, Silvan Käser, Fiona L. Kearns, Nathan R. Kern, Jeffery B. Klauda, Themis Lazaridis, Jinhyuk Lee, Justin A. Lemkul, Xiaorong Liu, Yun Luo, Alexander D. MacKerell, Dan Thomas Major, Markus Meuwly, Kwangho Nam, Lennart Nilsson, Victor Ovchinnikov, Emanuele Paci, Soohyung Park, Richard W. Pastor, Amanda R. Pittman, Carol Beth Post, Samarjeet Prasad, Jingzhi Pu, Yifei Qi, Thenmalarchelvi Rathinavelan, Daniel R. Roe, Benoı̂t Roux, Christopher N. Rowley, Jana Shen, Andrew C. Simmonett, Alexander J. Sodt, Kai Töpfer, Meenu Upadhyay, Arjan van der Vaart, Luis Itza Vazquez-Salazar, Richard M. Venable, Luke Warrensford, H. Lee Woodcock, Yujin Wu, Charles L. Brooks, Bernard R. Brooks, Martin Karplus,
Since its inception nearly a half century ago, CHARMM has been playing a central role in computational ... hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments ... occurred after 2009 when the last review of CHARMM was published. They include the following: new faster ... addition to providing the current snapshot of the CHARMM development, this review may serve as a starting ... tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research ...
Tópico(s): Enzyme Structure and Function
2024 - American Chemical Society | The Journal of Physical Chemistry B
Kolawole Sonibare, Lasantha Rathnayaka, Liqun Zhang,
... used forcefields, the Chemistry at Harvard Macromolecular Mechanics (CHARMM) forcefield and the Optimized Potentials for Liquid Simulations ... to compare the effectiveness of the forcefields. The CHARMM forcefield parameters for two smaller components —including n- ... and n-docosane (n-C22) predicted using the CHARMM forcefield to those from traditional OPLS-aa forcefield, ... 1,7-dimethylnaphthalene and n-docosane from the CHARMM and Nanoscale Molecular Dynamics (NAMD) program are very ... OPLS-aa forcefield and LAMMPS program. However, the CHARMM forcefield correctly predicted the crystallization of n-docosane ...
Tópico(s): Asphalt Pavement Performance Evaluation
2019 - Elsevier BV | Construction and Building Materials
Hao Liu, Song Dong, Hui Lü, Ray Luo, Haifeng Chen,
... s. Here, we report our development for the CHARMM community. Our residue‐specific IDP force field ( CHARMM 36 IDPSFF ) was developed based on the base ... of J‐couplings with previous work shows that CHARMM 36 IDPSFF and its corresponding base generic force field have their own advantages. In addition, CHARMM 36 IDPSFF simulations also agree with experiment for ... gyration of IDP s. Detailed analysis shows that CHARMM 36 IDPSFF can sample more diverse and disordered ...
Tópico(s): Enzyme Structure and Function
2018 - Wiley | Chemical Biology & Drug Design
Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, Alexander D. MacKerell, Jeffery B. Klauda, Wonpil Im,
... result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to ... lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) ... modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation ... protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable ...
Tópico(s): Spectroscopy and Quantum Chemical Studies
2015 - American Chemical Society | Journal of Chemical Theory and Computation
Michael F. Crowley, Mark J. Williamson, Ross C. Walker,
... s energy functional form with that of the CHARMM force field, gives the potential for direct translation ... nonbonding terms, along with their parameters, present in CHARMM topology and parameter files, with the intent of ... created a tool, CHAMBER, which can take a CHARMM protein structure file (PSF), coordinate file (COR) and ... a conversion route which enables the simulation of CHARMM parameterized models using AMBER's PMEMD engine; thus ... expended in ensuring a true representation of the CHARMM force field in AMBER providing energies and forces ...
Tópico(s): Advanced NMR Techniques and Applications
2009 - Wiley | International Journal of Quantum Chemistry
Philippe Ferrara, Holger Gohlke, D.J. Price, G. Klebe, Charles L. Brooks,
... complexes is presented. The scoring functions include the CHARMm potential, the scoring function DrugScore, the scoring function ... The role of solvation models in conjunction with CHARMm was explored in detail. These include a distance- ... to discriminate near-native from misdocked conformations, with CHARMm, DOCK-energy, DrugScore, ChemScore, and AutoDock yielding recognition ... going from decoy to cross-decoy recognition for CHARMm in the case of HIV-1 protease, whereas DrugScore and ChemScore, as well as CHARMm in the case of trypsin, show only small ...
Tópico(s): Click Chemistry and Applications
2004 - American Chemical Society | Journal of Medicinal Chemistry
Thomas B. Woolf, Alan Grossfield, John G. Pearson,
... phosphatidylcholine) membrane bilayer have been performed, using the CHARMM potential function. The CHARMM potential does not explicitly contain cation–π interactions: ... accuracy of the electrostatic effects present in the CHARMM parameter set. The current study compares the electrostatic interaction energy from CHARMM with calculations using the density functional program deMon. ... trajectories of indole and N-methylindole to compare CHARMM and deMon electrostatic energies. The results suggest that ...
Tópico(s): Molecular Sensors and Ion Detection
1999 - Wiley | International Journal of Quantum Chemistry
Adan Gallardo, Brandon M. Bogart, Bercem Dutagaci,
... using three commonly used force fields that are CHARMM c36m, AMBER ff14sb, and ff19sb. Simulations showed strong ... the AMBER force fields compared to that with CHARMM. Furthermore, we performed MD simulations of the complete elongation complex using CHARMM c36m and AMBER ff19sb force fields to compare ... Overall, our study showed that the differences between CHARMM and AMBER force fields strongly affect the dynamics of the nucleic acids. CHARMM provides highly flexible DNA, while AMBER largely stabilizes ...
Tópico(s): Bacteriophages and microbial interactions
2022 - American Chemical Society | Journal of Chemical Information and Modeling
Kye Won Wang, Jumin Lee, Han Zhang, Donghyuk Suh, Wonpil Im,
... long simulation time scales for large system sizes. CHARMM-GUI, a web-based platform, has been developed ... study describes an Implicit Solvent Modeler (ISM) in CHARMM-GUI for various generalized Born (GB) implicit solvent ... in different molecular dynamics programs such as AMBER, CHARMM, GENESIS, NAMD, OpenMM, and Tinker. The GB models ... OBC, GB-neck, GBMV, and GBSW with the CHARMM and Amber force fields for protein, DNA, RNA, ...
Tópico(s): Enzyme Structure and Function
2022 - American Chemical Society | The Journal of Physical Chemistry B
Jumin Lee, Manuel Hitzenberger, Manuel Rieger, Nathan R. Kern, Martin Zacharias, Wonpil Im,
... support diverse force fields and simulation programs in CHARMM-GUI, this work presents the development of FF- ... with various Amber force fields within the current CHARMM-GUI workflow. The currently supported Amber force fields ... necessary. The robustness and usefulness of this new CHARMM-GUI extension are demonstrated by two exemplary systems: ... system and a protein/DNA/RNA system. Currently, CHARMM-GUI supports the Amber force fields only for ...
Tópico(s): DNA and Nucleic Acid Chemistry
2020 - American Institute of Physics | The Journal of Chemical Physics
Brian H. Morrow, Judith A. Harrison,
... this work, the accuracy of three force fields (CHARMM, OPLS-AA, and TraPPE-UA) is assessed by ... too high compared to experiment; values using the CHARMM and OPLS-AA potentials tend to be more ... Simulations of binary mixtures show that both the CHARMM and TraPPE-UA potentials predict the same liquid- ... TraPPE-UA and only qualitatively reproduced by the CHARMM force field. Given the lack of phase equilibrium data used in the parameterization of the CHARMM potential, its ability to reproduce many aspects of ...
Tópico(s): Material Dynamics and Properties
2019 - American Chemical Society | Energy & Fuels
Baofu Qiao, S. Skanthakumar, L. Soderholm,
... for predicting stability, reactivity, and solubility. Herein, additive CHARMM force field parameters were developed to enable molecular ... much more resource-intensive polarizable AMOEBA potential, the CHARMM simulations reproduce the experimental hydration free energies and ... first-coordination sphere correlations for the Lu3+ ion (CHARMM only), but further improvement to both approaches is ... and Lu3+ coordination geometries are extracted from the CHARMM simulations and generally discussed in terms of potential ...
Tópico(s): Radioactive element chemistry and processing
2018 - American Chemical Society | Journal of Chemical Theory and Computation
... protein force fields (FFs) with TIP4P/Ice water, CHARMM, AMBER, and OPLS FFs were applied. CHARMM and AMBER FFs predict more β-sheet structure ... TmAFP-interface binding and antifreeze activity. In particular, CHARMM FF more clearly distinguishes the strengths of hydrogen ... other FFs, in agreement with experiments, implying that CHARMM FF can be a reasonable choice to simulate ... larger distances. These findings suggest the choice of CHARMM FF for AFP-TIP4P/Ice simulations and help ...
Tópico(s): Insect and Arachnid Ecology and Behavior
2018 - Public Library of Science | PLoS ONE
Zak E. Hughes, Tiffany R. Walsh,
... and apply a new polarizable force field, PdP-CHARMM, for the simulation of biomolecule–Pd binding under aqueous conditions. PdP-CHARMM was parametrized with density functional theory (DFT) calculations ... As part of our process for developing PdP-CHARMM, we provide an extensive study of the performance ... with best all-round performance to create PdP-CHARMM. We then employ PdP-CHARMM and metadynamics simulations to estimate the adsorption free ...
Tópico(s): Ion-surface interactions and analysis
2018 - American Chemical Society | The Journal of Physical Chemistry C
Josh V. Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, Axel Kohlmeyer,
... between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there ... tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to ... GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable ... the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. The newly available automatic conversion ...
Tópico(s): Enzyme Structure and Function
2016 - American Chemical Society | Journal of Chemical Information and Modeling
Sunhwan Jo, Xi Cheng, Shahidul M. Islam, Lei Huang, Huan Rui, Allen Zhu, Hui Sun Lee, Yifei Qi, Wei Han, Kenno Vanommeslaeghe, Alexander D. MacKerell, Benoı̂t Roux, Wonpil Im,
CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the ... techniques. Since it is originally developed in 2006, CHARMM-GUI has been widely adopted for various purposes ... describe functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator, such as ligand force field ...
Tópico(s): Advanced NMR Techniques and Applications
2014 - Elsevier BV | Advances in protein chemistry and structural biology
Emilia L. Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin Song, Eder M. Dávila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje‐Galvan, Richard M. Venable, Jeffery B. Klauda, Wonpil Im,
CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems ... based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD ... of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for ...
Tópico(s): Nanopore and Nanochannel Transport Studies
2014 - Wiley | Journal of Computational Chemistry
Sunhwan Jo, Wei Jiang, Hui Sun Lee, Benoı̂t Roux, Wonpil Im,
... Here, we present a user-friendly Web interface, CHARMM-GUI Ligand Binder (http://www.charmm-gui.org/input/gbinding), to provide standardized CHARMM input files for calculations of absolute binding free ... previous computational studies (within ∼2 kcal/mol). Therefore, CHARMM-GUI Ligand Binder provides a convenient and reliable ...
Tópico(s): Enzyme Structure and Function
2012 - American Chemical Society | Journal of Chemical Information and Modeling
Pär Bjelkmar, Per Larsson, Michel A. Cuendet, Berk Hess, Erik Lindahl,
... specifically for it. We have here implemented the CHARMM force field and all necessary extended functional forms in the GROMACS molecular simulation package, to make CHARMM-specific features available and to test them in ... hydrogens. The implementation has full support both for CHARMM-specific features such as multiple potentials over the ... different models for water representation, including comparisons between CHARMM and traditional TIP3P. Including the correction maps improves ...
Tópico(s): Enzyme Structure and Function
2010 - American Chemical Society | Journal of Chemical Theory and Computation
Priyanka Prakash, Ramasubbu Sankararamakrishnan,
... force field and three versions of all‐atom CHARMM force fields. Three different systems consisting of 48, ... calculated from Berger and the recent versions of CHARMM simulations have shown generally good agreement with the ... are also observed in several headgroup parameters between CHARMM and Berger simulations. Our results demonstrate that when changes were introduced to improve CHARMM force field using PME scheme, all the headgroup ... in phospholipids require refinement for both Berger and CHARMM force fields. © 2009 Wiley Periodicals, Inc.J Comput ...
Tópico(s): Protein Structure and Dynamics
2009 - Wiley | Journal of Computational Chemistry