ADL: Rigid file has flexible residues?
ksharma997 at gmail.com
Wed Jun 24 04:05:00 PDT 2015
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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