Hi all,
There are two big questions here. I am extremely grateful for even the smallest contribution that yields a result.
This is concerning Raccoon(1) original, not Raccoon2. The original Raccoon allows your current workstation to perform VS, the new Raccoon2 does not it must be a cluster with PBS queue).
I have two questions:
1) I performed an active site prediction using AutoLigand. From the results I have a site of potential interest, "#Option 7" from a calculation performed with 400 points. When I now come to perform a drug VS on the receptor, how do I specify the location of the potential site on the receptor? I do not want VS to scan the whole surface, only the site I had identified earlier.
I have tried to generate a map file for the receptor target. This is done by loading the target into AutoDockTools, loading in the predicted target .pdb. Building a grid box around the predicted site. However, when I save the grid output as a .gpf file, Raccoon will not accept this map file for the receptor. I see the error:
Map file not found! The .fld map is missing. Select another directory.
(A) Which tool generates the .fld file? (B) Why aren't these generated automatically by ADT? (C) Why does the save .gpf file reference e.g., map._for_docking.A.map yet these files do not exist?
2) I'm running Raccoon(1) along with the latest of AutoDockTools, AutoDock and AutoDock tools. Within Raccoon(1), when I've specified Ligand(s), Receptor(s), Maps, and Docking (all are green), I come to execute "G E N E R A T E" and I'm faced with the error:
Impossible to calculate the cached maps here:
C:/Users/.........\maps
GIVING UP...
Any idea why?
Why is it impossible to calculate the cached maps? No explanation is offered, only the somewhat dire and very unhelpful statement "GIVING UP...".
3) If I select "at each job" for the map generation, I end up with a slightly different error:
Impossible to create the directory:
None
GIVING UP...
Again, not much information to go on. I suspect having seen a post back in 2013 that the problems in (2) and (3) are related to incorrect atom-types in the ligand when generating maps/
Run autogrid to generate the .map and .fld files. autogrid4 -p -l
within the .gpf file mention which map files you want. e.g.,
gridfld .maps.fld # grid_data_file
map .A.map # atom-specific affinity map
elecmap .e.map # electrostatic potential map
dsolvmap .d.map # desolvation potential map
Uttam Pal A few things I've figured out. AutoDockTools will not generate all the map files Raccoon expects. I need to add additional e.g., .Br.map by hand even though the receptor does not contain that atom type.
But that aside, I'm still getting lots of problem. Please see this question to:
https://www.researchgate.net/post/Autodock_Raccoon-why_is_it_throwing_a_python_error
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