Okamoto, "Optimisation of OPLS-UA force- field parameters for protein systems using protein data bank," Molecular Simulation, vol. 36, no. 14, pp. 1148-1156, 2010.Optimisation of OPLS-UA force-field parameters for protein systems using protein data bank. Sakae, Yoshitake,Okamoto, Yuko. ...
We have previously proposed a method for refining force-field parameters of protein systems, which consists of minimising the summation of the square of the force acting on each atom in the proteins with the structures from the protein data bank (PDB). The results showed that the modified force...
Revisiting OPLS force field parameters for ionic liquid simulations. J. Chem. Theory Comput. 2017, 13 (12), 6131 6145.Feng G., Huang J., Sumpter B. G., Meunier V., Qiao R. Structure and dynamics of electrical double layers ... IS Vovchynskyi,O Kalugin - 《Kharkov University Bulletin...
If you want to use pdb2gmx to automatically generate your topology, you have toensure that the appropriate .rtp entry is present within the desired force fieldand has the same name as the building block you are trying to use (again, thisis spelled out in Chapter 5 of the manual). If ...
# and a separate ID for looking up 4-body improper interaction parameters # The complete @atom type name includes ALL of these ID numbers. There's # no need to force the end-user to type the complete name of each atom. # The "replace" command used below informs moltemplate that the ...
Force Field Builder Efficient tool for optimizing custom torsion parameters in OPLS4 MS Transport Efficient molecular dynamics (MD) simulation tool for predicting liquid viscosity and diffusions of atoms and molecules Materials Science MS CG Efficient coarse-grained (CG) molecular dynamics (MD) simulation...
Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the ...
Force fields - Gromacswww.gromacs.org/user_contributions.html 19SB原文也已发表,见 ff19SB: Amino-acid specific protein backbone parameters trained against quantum mechanics energy surfaces in solutionpubs.acs.org/doi/10.1021/acs.jctc.9b00591编辑...
The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any ...
Comparison with NMR Parameters Most biomolecular force fields are well-suited for studying static properties of equilibrium structures; however, they have hardly been tested on very-long... VDS David,E Lindahl - 《Journal of Physical Chemistry B》 被引量: 105发表: 2003年 Comparison of Protein ...