Even after specifying the flexible residues in the ligand file when I go ahead to save it as flexible pdbqt the prog says- " Must Specify Residues for flexible side chains or set hinge". Can anyone please tell me where I am going wrong? How can I set a hinge?
Also when I try to set the Grid Map, while choosing ligand the error message comes as it is not getting saved in the previous steps - "can only select molecule with written Autotor pdbqt output file".
Here i am listing major steps for Autodock 4.2 for site directed docking.
1. Macro molecule Preparation by adding Hydrogen and kollman charges.
2. Ligand torsion and rotamer library preparation by counting rotatable bonds. Save this file as ligand pdbqt
3. Flexible residues assignment and torsion count.
4. Grid map assignment and log generation
5. Dockng parameter assignment and log generation
6. Docking calculation execution.
7. Result analysis by Docking Log file analysis.
Check where you are deviating.
Sounds awkward (Flexible residues in ligand.) Well after assigning flexibility to ligand you also have to assign flexibility in protein. Use Select >> 'Select from string' option to select residues of proteins you want to consider as flexible. Go to Flexible residues >> 'Choose torsions in currently selected residues' after selecting your protein molecule from Input.
Setting grid maps requires protein autotors files also and without it you can not move beyond.
Autodock 4.2 uses autotors files of both lignad and protein. Define both first before starting any calculations.
@ Rajnikant Namdeo- initially i had tried creating rigid file for the ligand . Then also I was getting the same error "Flexible residues or hinge must be specified" . After that only I went on to creating the flexible file for ligand.
and I tried that too but didn't help.. while i am setting the grid. Grid>>Set map Types>>Choose ligand . it is giving the same error message "Can Only Select Molecule with written autotors pdbqt output file"
Here i am listing major steps for Autodock 4.2 for site directed docking.
1. Macro molecule Preparation by adding Hydrogen and kollman charges.
2. Ligand torsion and rotamer library preparation by counting rotatable bonds. Save this file as ligand pdbqt
3. Flexible residues assignment and torsion count.
4. Grid map assignment and log generation
5. Dockng parameter assignment and log generation
6. Docking calculation execution.
7. Result analysis by Docking Log file analysis.
Check where you are deviating.
so is it that for the Ligand as well as Receptor steps 1 to 3 are same .. ???? there is no change in the steps ??
i hav used the same steps as mentioned by you.... but didn't add kollman charges wil try to do that also . Thanks !
Kollman charges are meant for protein file only. For ligand use "Ligand" tab section of MGL Tools for preparing your ligand PDBQT file.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics