I have done docking of 2 ligands with pyrx and selected two best poses with maestro but now I want pdb file of that complex bcz in gromacs the first command is pdb2gmx .So how to get pdb file of that pose. is there any other way plz let me knw.
After docking with PyRx, firstly select the docking pose, you want to investigate further from the "Analysing results" tab at the bottom of the window. Now, go to the Navigator panel (upper-left side), and right click on the ligand and select "Save as PDB".
Now you can concatenate the protein and ligand files into a single protein-ligand complex file using PyMol/ Discovery Studio/ VMD or even, by manually adding the ligand coordinates at the end of the protein pdb file.
When we are clicking on the "save as PDB" in pyrx that will not contain all the information of docked ligand and protein. why are further opening in other software just to visualize it.
Dear Kaur,
You can select both the file protein and ligand and merge them. Now you will have one new file that will be complex of protein-ligand. You can use Schrodinger's maestro for this taks.
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