We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ∼900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles, and torsional angles and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields and indications for how to design improved force fields. The torsional degrees of freedom are the main contribution to conformational changes of atomic charges and molecular dipole moments, but indirect effects due to change in bond distances and angles account for ∼25% of the ...
Statistical analysis of coil regions in protein structures has been used to obtain the local backbon...
Chuan Tian presented his work on Amber ff19SB force field at the Chodera lab at MSKCC on Sep 12, 201...
The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to ass...
We apply a model for analyzing the importance of conformational charge flux to 11 molecules with the...
We apply a model for analyzing the importance of conformational charge flux to 11 molecules with the...
The applicability of molecular dynamics simulations for studies of protein folding or intrinsically ...
The applicability of molecular dynamics simulations for studies of protein folding or intrinsically ...
The applicability of molecular dynamics simulations for studies of protein folding or intrinsically ...
The applicability of molecular dynamics simulations for studies of protein folding or intrinsically ...
We assess the accuracy of force field (FF) electrostatics at several levels of approximation from th...
The local conformational (phi, chi, chi) preferences of amino acid residues remain an active researc...
The local conformational (phi, chi, chi) preferences of amino acid residues remain an active researc...
Abstract: We present the derivation of a new molecular mechanical force field for simulating the str...
We have studied the conformational dependence of molecular mechanics atomic charges for proteins by ...
We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipe...
Statistical analysis of coil regions in protein structures has been used to obtain the local backbon...
Chuan Tian presented his work on Amber ff19SB force field at the Chodera lab at MSKCC on Sep 12, 201...
The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to ass...
We apply a model for analyzing the importance of conformational charge flux to 11 molecules with the...
We apply a model for analyzing the importance of conformational charge flux to 11 molecules with the...
The applicability of molecular dynamics simulations for studies of protein folding or intrinsically ...
The applicability of molecular dynamics simulations for studies of protein folding or intrinsically ...
The applicability of molecular dynamics simulations for studies of protein folding or intrinsically ...
The applicability of molecular dynamics simulations for studies of protein folding or intrinsically ...
We assess the accuracy of force field (FF) electrostatics at several levels of approximation from th...
The local conformational (phi, chi, chi) preferences of amino acid residues remain an active researc...
The local conformational (phi, chi, chi) preferences of amino acid residues remain an active researc...
Abstract: We present the derivation of a new molecular mechanical force field for simulating the str...
We have studied the conformational dependence of molecular mechanics atomic charges for proteins by ...
We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipe...
Statistical analysis of coil regions in protein structures has been used to obtain the local backbon...
Chuan Tian presented his work on Amber ff19SB force field at the Chodera lab at MSKCC on Sep 12, 201...
The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to ass...