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PostPosted: Sun Jun 08, 2014 6:23 am 
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Hi
I am docking on receptor 2HA2 on MGLTools 1.5.6rc3 on ubuntu 13. I am taking chain A and have removed the crystallized ligand SCK and trying to redock it. I have selected ASP74 as flexible in select from string. While selecting the choose torsions in currently selected residues, I am getting this error in red:
AttributeError: Residue instance has no attribute 'torscount'

After going through archives I found few mails on this but no solutions....
Could anyone advice please...


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PostPosted: Tue Jun 10, 2014 2:33 am 
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Could anyone help in this regard. I am stuck!


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PostPosted: Tue Jun 10, 2014 6:25 pm 
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Please compare the steps you are using in ADT with these:
1. import 2ha2.pdb into ADT (either using File->Import->Fetch From Web OR File->Read Molecule if you already have a local copy of 2ha2.pdb)

2. clean up 2ha2.pdb:
-remove water
Edit-> Delete Water
-remove chain B (??unless you want to model flexible residues in each chain??)
Select->Select_from String
Chain B, Atom '*'
Add
Edit->Delete-> Delete Selected Atoms
[ -remove hetatms (same as removing water except choose Atom Sets.. 'hetatm' in Atom Sets... list)]

3. Save 2ha2 as a pdbqt file:
Edit->Hydrogens Add
Grid->Macromolecule->Choose...
[save as 2ha2.pdbqt]

4. Next use Select->Select from String: type "ASP74" in the Residue entry and click Add.

5. in ADT under Flexible Residues
-Input-> Choose Macromolecule .... select '2ha2' + click 'Select Molecule'
(click ok + ignore the Warning Message that opens)
-Choose Torsions in Currently Selected Residues...
(this lets you turn off one of the the rotatable bonds if you want to ... ok to leave as is)
click Close

- FINALLY, use
-Output-> Save Flexible PDBQT... (to write residues with rotatable bonds)
-Output-> Save Rigid PDBQT... (to write the rigid residues)


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