J Chem Inf Model - Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

Tópicos

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Resumo

Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug candidates interacting with biological systems. In these simulations, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and partial atomic charges is required. In the present article, algorithms for the assignment of parameters and charges for the CHARMM General Force Field (CGenFF) are presented. These algorithms rely on the existing parameters and charges that were determined as part of the parametrization of the force field. Bonded parameters are assigned based on the similarity between the atom types that define said parameters, while charges are determined using an extended bond-charge increment scheme. Charge increments were optimized to reproduce the charges on model compounds that were part of the parametrization of the force field. A "penalty score" is returned for every bonded parameter and charge, allowing the user to quickly and conveniently assess the quality of the force field representation of different parts of the compound of interest. Case studies are presented to clarify the functioning of the algorithms and the significance of their output data.

Resumo Limpo

molecular mechan forc field wide use computeraid drug design studi drug candid interact biolog system simul biolog part typic repres special biomolecular forc field drug repres match general organ forc field order appli general forc field arbitrari druglik molecul function assign atom type paramet partial atom charg requir present articl algorithm assign paramet charg charmm general forc field cgenff present algorithm reli exist paramet charg determin part parametr forc field bond paramet assign base similar atom type defin said paramet charg determin use extend bondcharg increment scheme charg increment optim reproduc charg model compound part parametr forc field penalti score return everi bond paramet charg allow user quick conveni assess qualiti forc field represent differ part compound interest case studi present clarifi function algorithm signific output data

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