Hi, I want to use a modified Autodock grid map in docking calculations with smina.
The problem is that I don't know which type of file I have to put as the argument of the command user_grid.
I tried with the file .maps.fld and with the map of the specific atom type I'm interested in, but it didn't work.
I would be grateful if you could help me.
Thanks,
Ivan
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Sorry to take so long to respond - I was on vacation and had very little internet access.
With the user_grid option (which I haven’t used for a long time), you can specify a single grid. If the ligand overlaps a point in the grid, the value at that point is added to the total score. It is not atom type specific - every atom of the ligand is considered when calculating the overlap.
Hi, I want to use a modified Autodock grid map in docking calculations with smina.
The problem is that I don't know which type of file I have to put as the argument of the command user_grid.
I tried with the file .maps.fld and with the map of the specific atom type I'm interested in, but it didn't work.
I would be grateful if you could help me.
Thanks,
Ivan
Hi, I want to use a modified Autodock grid map in docking calculations with smina.
The problem is that I don't know which type of file I have to put as the argument of the command user_grid.
I tried with the file .maps.fld and with the map of the specific atom type I'm interested in, but it didn't work.
I would be grateful if you could help me.
Thanks,
Ivan
Hi Ivan,
Sorry to take so long to respond - I was on vacation and had very little internet access.
With the user_grid option (which I haven’t used for a long time), you can specify a single grid. If the ligand overlaps a point in the grid, the value at that point is added to the total score. It is not atom type specific - every atom of the ligand is considered when calculating the overlap.
The file format is the AutoDock Grid Map format described on page 36 of the user guide:
http://autodock.scripps.edu/faqs-help/manual/autodock-4-2-user-guide/AutoDock4.2.6_UserGuide.pdf
Hope this helps,
David Koes
Assistant Professor
Computational & Systems Biology
University of Pittsburgh
On Jun 13, 2018, at 9:17 AM, Ivan Felsztyna ivanfelsztyna@users.sourceforge.netamp#105;amp#118;amp#97;amp#110;amp#102;amp#101;amp#108;amp#115;amp#122;amp#116;amp#121;amp#110;amp#97;amp#64;amp#117;amp#115;amp#101;amp#114;amp#115;amp#46;amp#115;amp#111;amp#117;amp#114;amp#99;amp#101;amp#102;amp#111;amp#114;amp#103;amp#101;amp#46;amp#110;amp#101;amp#116; wrote:
Hi, I want to use a modified Autodock grid map in docking calculations with smina.
The problem is that I don't know which type of file I have to put as the argument of the command user_grid.
I tried with the file .maps.fld and with the map of the specific atom type I'm interested in, but it didn't work.
I would be grateful if you could help me.
Thanks,
Ivan
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