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PostPosted: Thu Feb 07, 2013 10:07 pm 
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Joined: Mon Feb 04, 2013 3:25 am
Posts: 5
Hi all,

I am new to the usage of Vina (first time using). I used the following config file

receptor = xxxx_rigid.pdbqt
flex = xxxx_flex.pdbqt
ligand = ligand_only_cropped_xd1.pdbqt

out = xxxx_all.pdbqt

center_x = 37.408
center_y = -13.631
center_z = -31.410

size_x = 34
size_y = 54
size_z = 34
exhaustiveness = 16


My problem is in my output file (xxxx_all.pdbqt) the solutions NOT ONLY CONTAIN THE LIGAND BUT ALSO THE FLEXIBLE RESIDUES. Is this normal behavior or have I done something wrong?

Thank you

Sajeewa Dewage


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PostPosted: Wed Feb 13, 2013 6:12 pm 
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Joined: Fri Sep 21, 2012 3:25 am
Posts: 40
Location: Mexico
Yeap, that is normal.


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PostPosted: Sat Jul 13, 2013 3:34 am 
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Joined: Fri Sep 21, 2012 3:25 am
Posts: 40
Location: Mexico
That is the normal behavior.

sajeewasp wrote:
Hi all,

I am new to the usage of Vina (first time using). I used the following config file

receptor = xxxx_rigid.pdbqt
flex = xxxx_flex.pdbqt
ligand = ligand_only_cropped_xd1.pdbqt

out = xxxx_all.pdbqt

center_x = 37.408
center_y = -13.631
center_z = -31.410

size_x = 34
size_y = 54
size_z = 34
exhaustiveness = 16


My problem is in my output file (xxxx_all.pdbqt) the solutions NOT ONLY CONTAIN THE LIGAND BUT ALSO THE FLEXIBLE RESIDUES. Is this normal behavior or have I done something wrong?

Thank you

Sajeewa Dewage


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 Profile  
 
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