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PostPosted: Tue Sep 01, 2009 10:23 pm 
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Hello,

When trying to save certain PDB files as a PDBQT I run into one of the following two issues. First if I follow the procedure for setting up a ligand as oulined in the file Using Autodock 4 with Autodocktools: A tutorial (i.e. ligand-->output-->save as PDBQT ), it generats PDBQT files that lack certain information such as connectivity information.(I know with ab-initio computational calculations only the positions of the nuclei matter not the imaginary bonds but this is different right?). The other problem I have is if I try to save the ligand by bypassing this step and simply going to file-->save-->write PDBT and I save the file including the connectivity there is an issue when I try to run Autodock which says that " all atom and hetatm records must be given before any nested braches; see line 2 in PDBT file '(ligand file name.pdbqt)' ". EDIT: I just figured out by adding the lines ROOT and ENDROOT I can get the file to be used by autodock but Does the PDBQT file need to contain information about which bonds are rotable etc? or should it only contain geometries and connectivities?

Thanks.

-David


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PostPosted: Wed Nov 11, 2009 6:43 am 
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When you prepare the ligand, you are supposed to choose/detect a root and assign torsions. After which saving it as
PDBQT file is not a problem at all. The PDBQT file will have all the root information and the torsion details in it.


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PostPosted: Mon Jan 12, 2015 7:07 am 
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ssarchana wrote:
When you prepare the ligand, you are supposed to choose/detect a root and assign torsions. After which saving it as
PDBQT file is not a problem at all. The PDBQT file will have all the root information and the torsion details in it.

when i save any pdbqt file, save with lock sign in windows. i just want to save them in simple format. i am doing docking in windows by using autodock 4.2. please give me suggestion that how can i remove lock sign.


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