Hi all,
I'm trying to use AutoDock Flexible Receptor (ADFR) to do a flexible docking between a membrane protein and its ligand. I already got some candidate poses, and I'd like to validate them using molecular dynamics with a software like GROMACS.
The issue I have is that flexible docking alters the initial conformation of the protein since the flexible residues are allowed to move. Therefore, is there a way to merge the conformation of the flexible residues and the initial protein structure? I need both ligand and protein (with the flexible residues in their final conformation) to run the simulation. Any ideas?
Thanks,
To merge flexible residues with the initial protein structure, you can use the final conformation from ADFR and replace the corresponding flexible residues in the original protein structure before running GROMACS. Ensure proper atom alignment and energy minimization to avoid structural conflicts.
Try to combine the flexible residues with your original protein structure, align the final conformation from ADFR with the starting structure. Then, refine it in GROMACS before running the MD simulation. Hope it works.
To merge the flexible docking conformation from ADFR with the initial protein structure for GROMACS:
Ensure proper equilibration and validation before MD.
all of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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