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PostPosted: Sun Oct 27, 2013 3:19 pm 
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I am running MGL_Tools v-1.5.7rc1 Mar_28_13 and have a couple of questions about the Tutorial.

1. Exercise 4. Has a FYI about some pull-down menu choices for placing the grid box. How does the ligand get chosen in order to center the grid box on the ligand?

2. In running the Tutorial I have noticed that when I select the menu option to Edit dpf in the Docking pull-down menu the number of torsions has been set to 14 although I followed the instruction in Exercise 2 to set the number of torsions to 6.

3. When should one select Gasteiger charges rather than Kollman charges?

Thanks in advance.


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PostPosted: Tue Oct 29, 2013 4:24 pm 
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1. "How does the ligand get chosen in order to center the grid box on the ligand?"
It gets chosen either with:
Grid->Set Map Types-> Choose Ligand...
OR:
Grid->Set Map Types-> Open Ligand...

2. "In running the Tutorial I have noticed that when I select the menu option to Edit dpf in the Docking pull-down menu the number of torsions has been set to 14 although I followed the instruction in Exercise 2 to set the number of torsions to 6."

Dpf files contain the keyword torsdof plus a value. Torsdof, the total number of torsional degrees of freedom, is the total number of possible torsions in the input ligand not the actual number of active torsions in the ligand pdbqt file. So what you see in the dpf is correct.


3."When should one select Gasteiger charges rather than Kollman charges?"
If you are using any version of autodock4, always select Gasteiger charges.
If you are using autodock3, select Kollman charges.


Last edited by Ruth Huey on Thu Dec 12, 2013 5:33 pm, edited 1 time in total.

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PostPosted: Tue Oct 29, 2013 6:59 pm 
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Ruth

Thanks for the reply.

I can now select the ligand for the center o the Grid Box.

As far as the number of the ligand degrees of freedom is concerned, it doesn't seem to matter how I select the ligand the ligand dpf file still shows 14 as the number of active torsions in the ligand.

Another thing that I've noticed is that only one of cores of my Intel Core i5 quad core processor is involved in the calculation. Now if I run PyRx as the gui it finds three of the four cores in the cpu. Does this make any sense?

Again. thanks in advance.

S. Molnar


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PostPosted: Wed Oct 30, 2013 12:08 pm 
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The hsg1.dpf file is attached.


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hsg1.dpf [2.89 KiB]
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PostPosted: Tue Dec 10, 2013 7:22 pm 
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The number of active torsions (i.e. bonds treated as rotatable) in the ligand can be changed in ADT with:
Ligand->Torsion Tree->Choose Torsions...
--Opens the Torsion Count widget and changes the coloring of the bonds in the displayed ligand. At first, rotatable bonds in the ligand are green and non-rotatable bonds are red. While this widget is open, holding down the Shift key while clicking on a green-bond (active torsion) in the ligand changes that bond to purple (inactive torsion) and vice-versa. [Red bonds are never rotatable].
OR
Ligand->Torsion Tree->Set Number of Torsions..
--Opens the Set Number of Active Torsions widget displaying the current number of active torsions in the ligand (and colors the displayed bonds as described above). This widget supports setting the number of active torsions. It also provides the choice of keeping the torsions that move the fewest atoms or those that move the most atoms.


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