Improved CHARMM Additive Force Field Parameters to Accurately Model Tyrosine-Choline Cation-π Interactions
نویسندگان
چکیده
منابع مشابه
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
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 of chemical groups present in biomolecules and drug-like molecules, including a large number of he...
متن کاملCHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded in...
متن کاملCation–π–cation interactions in structural biology
Biological structures are stabilized by a variety of noncovalent interactions, such as hydrogen bonds, π –stacking, salt bridges or hydrophobic interactions. Besides hydrogen bonds and π– stacking, cation–π interactions between aromatic rings and positively charged groups have emerged as one of the most important interactions in structural biology. Although the role and energetic characteristic...
متن کاملAdditivity of Cation-π Interactions: An ab Initio Computational Study on π-Cation-π Sandwich Complexes
Center for Drug DiscoVery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 DoVer Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science...
متن کاملCHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes
Force field parameters specifically optimized for residues important in the study of RNA catalysis are derived from density-functional calculations, in a fashion consistent with the CHARMM27 all-atom empirical force field. Parameters are presented for residues that model reactive RNA intermediates and transition state analogs, thio-substituted phosphates and phosphoranes, and bound Mg(2+) and d...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2017
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2016.11.975