Geometry optimization of the ADB linkers

RH Ritesh Haldar
MJ Marius Jakoby
AM Antoine Mazel
QZ Qiang Zhang
AW Alexander Welle
TM Tawheed Mohamed
PK Peter Krolla
WW Wolfgang Wenzel
SD Stéphane Diring
FO Fabrice Odobel
BR Bryce S. Richards
IH Ian A. Howard
CW Christof Wöll
request Request a Protocol
ask Ask a question
Favorite

Parameters for ADB ligand are obtained from LigParGen web server3638, LigGerGen provides bond, angle, dihedral, and Lennard-Jones OPLS-AA parameters with 1.14*CM1A or 1.14*CM1A-LBCC partial atomic charges. For charged molecules (ADB linker with net charge -2) CM1A charges are NOT scaled by a factor 1.14.

ADB linker is preoptimized based on the OPLS-AA Force Field, duplicate and move the optimized ligand up by 6 Å, freeze (their X, Y, and Z position will not be updated) skeleton carbon atoms (Supplementary Fig. 11) and optimize the dimer in GROMACS.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A