CHARMM: the biomolecular simulation program
BR Brooks, CL Brooks III… - Journal of …, 2009 - Wiley Online Library
Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …
widely used molecular simulation program. It has been developed over the last three …
Development and current status of the CHARMM force field for nucleic acids
AD MacKerell Jr, N Banavali… - … : original Research on …, 2000 - Wiley Online Library
The CHARMM27 all‐atom force field for nucleic acids represents a highly optimized model
for investigations of nucleic acids via empirical force field calculations. The force field …
for investigations of nucleic acids via empirical force field calculations. The force field …
Assessing the current state of amber force field modifications for DNA
R Galindo-Murillo, JC Robertson… - Journal of chemical …, 2016 - ACS Publications
The utility of molecular dynamics (MD) simulations to model biomolecular structure,
dynamics, and interactions has witnessed enormous advances in recent years due to the …
dynamics, and interactions has witnessed enormous advances in recent years due to the …
Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles
M Zgarbová, M Otyepka, J Sponer… - Journal of chemical …, 2011 - ACS Publications
We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force
field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 …
field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 …
Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational …
AD Mackerell Jr, M Feig… - Journal of computational …, 2004 - Wiley Online Library
Computational studies of proteins based on empirical force fields represent a powerful tool
to obtain structure–function relationships at an atomic level, and are central in current efforts …
to obtain structure–function relationships at an atomic level, and are central in current efforts …
Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium
K Hart, N Foloppe, CM Baker, EJ Denning… - Journal of chemical …, 2012 - ACS Publications
The B-form of DNA can populate two different backbone conformations: BI and BII, defined
by the difference between the torsion angles ε and ζ (BI= ε–ζ< 0 and BII= ε–ζ> 0). BI is the …
by the difference between the torsion angles ε and ζ (BI= ε–ζ< 0 and BII= ε–ζ> 0). BI is the …
[HTML][HTML] Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers
We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field,
where emphasis has been made on the correct representation of the α/γ concerted rotation …
where emphasis has been made on the correct representation of the α/γ concerted rotation …
All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
N Foloppe, AD MacKerell, Jr - Journal of computational …, 2000 - Wiley Online Library
Empirical force‐field calculations on biological molecules represent an effective method to
obtain atomic detail information on the relationship of their structure to their function. Results …
obtain atomic detail information on the relationship of their structure to their function. Results …
Empirical force fields for biological macromolecules: overview and issues
AD MacKerell Jr - Journal of computational chemistry, 2004 - Wiley Online Library
Empirical force field‐based studies of biological macromolecules are becoming a common
tool for investigating their structure–activity relationships at an atomic level of detail. Such …
tool for investigating their structure–activity relationships at an atomic level of detail. Such …
All‐atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
AD MacKerell Jr, NK Banavali - Journal of computational …, 2000 - Wiley Online Library
Molecular dynamics simulations based on empirical force fields can greatly enhance
knowledge of DNA and RNA structure and dynamics in solution. Presented are results on …
knowledge of DNA and RNA structure and dynamics in solution. Presented are results on …