ADL: Rigid file has flexible residues?

kanika sharma ksharma997 at
Wed Jun 24 04:05:00 PDT 2015

Hello All,

I followed the tutorial to prepare files in Autodock and prepared the
flexible residues file followed by  saving the same molecule as  :

Grid → Macromolecule → Open → X.pdb.

1. Flexible residues → Input → Choose molecule → X.pdb

2. Select the residues to be flexible: Select → Select from string → ASP112
→ Add → (followed by same for ASP202 and TRP 296).

3. Flexible residues → Choose torsions in currently selected residues →
[click on rotatable bonds to inactivate them, or vice versa].

4. Flexible residues → Output → Save flexible PDBQT → [save as

5. Flexible residues → Output → Save rigid PDBQT → [save as X_rigid.pdbqt].

The issue I am trying to understand is why does my X_rigid.pdbqt have these
residues (ASP112, ASP202 and TRP 296)...? They are selected as flexible
then shouldn't they be not present in rigid file?

Please correct if my thought is wrong


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