I have performed the Molecular Docking using ADFR suite, I have obtained the files in _out.pdbqt format for ligand docked poses, upon inspection, both visually and reading the pdbqt files of ligand, I have found that there are flexible residues of protein present in ligand docked pose. Now I want to make the complex of the docked pose with the protein structure to go for MD simulation, however, I am not sure how to do that as the rigid receptor file of the protein also contains the residues which are present in the ligand file. If anyone knows how can I combine the ligand and protein file into a single complex so that the flexible residues position from the ligand file can get appened/fixed in protein structure so I do not get double same residues in the complex. Kindly let me know. If any more information is required, I am also happy to provide more details about that.
Talha Islam
Assalam o alaikum wa rahmatullahi wa barkatuhu
Firstly, You open your protein in pymol and ligand out file. check your lead conformation of liagnd with protein select the export molecule option then save .pdb file.
Waseem Ahmad Ansari Thank you for your answer, but the problem is that in my ligand out file, there are some residues from protein which I selected to remain flexible in docking, and there are two other protein files, one with rigid receptor and one for receptor with flexible residues. My problem is about combining all three files into a single molecule with the overlapping of the residues in ligand and protein files.