ADL: Autodock problem for Grid generation

bagdevi.mishra at gmail.com bagdevi.mishra at gmail.com
Thu Apr 2 00:38:11 PDT 2009


You prepare your GPF file, using any one ligand, and then edit it manually
by adding maps for all atom types, in all the ligands.

if your first GPF file is as follows:

npts 40 30 40                        # num.grid points in xyz
gridfld receptor.maps.fld            # grid_data_file
spacing 0.375                        # spacing(A)
receptor_types A C N NA OA SA        # receptor atom types
ligand_types A HD N NA OA            # ligand atom types
receptor receptor.pdbqt              # macromolecule
gridcenter 20.837 106.749 49.927     # xyz-coordinates or auto
smooth 0.5                           # store minimum energy w/in rad(A)
map receptor.A.map                   # atom-specific affinity map
map receptor.HD.map                  # atom-specific affinity map
map receptor.N.map                   # atom-specific affinity map
map receptor.NA.map                  # atom-specific affinity map
map receptor.OA.map                  # atom-specific affinity map
elecmap receptor.e.map               # electrostatic potential map
dsolvmap receptor.d.map              # desolvation potential map
dielectric -0.1465                   # <0, AD4 distance-dep.diel;>0,
constant

you can add more maps to it as follows:

npts 40 30 40                        # num.grid points in xyz
gridfld receptor.maps.fld            # grid_data_file
spacing 0.375                        # spacing(A)
receptor_types A C N NA OA SA        # receptor atom types
ligand_types A HD N NA OA CL F           # ligand atom types
receptor receptor.pdbqt              # macromolecule
gridcenter 20.837 106.749 49.927     # xyz-coordinates or auto
smooth 0.5                           # store minimum energy w/in rad(A)
map receptor.A.map                   # atom-specific affinity map
map receptor.HD.map                  # atom-specific affinity map
map receptor.N.map                   # atom-specific affinity map
map receptor.NA.map                  # atom-specific affinity map
map receptor.OA.map                  # atom-specific affinity map
map receptor.CL.map
map receptor.F.map
elecmap receptor.e.map               # electrostatic potential map
dsolvmap receptor.d.map              # desolvation potential map
dielectric -0.1465                   # <0, AD4 distance-dep.diel;>0,
constant

As you can see above, you need to add the changed at two different places,
first at
# ligand atom types
and then at
# atom specific affinity map

Hope this helps.


Regards,
Bagdevi Mishra.




On Wed, Apr 1, 2009 at 9:03 PM, Haipeng hU <hhu2 at emory.edu> wrote:
> Hi,
>
>     I just begin to use autodock to do some molecular docking. I met a
problem in the grid generation step. In the tutorial, you should 'set map
types' based on a ligand when preparing the GPF file. Is that means I should
generate a grid file for each of my ligand, since I have a bounch of ligands
need to be docked into the same binding site of a macromolecule. If not,
some of my ligand contain CL or F atoms, so there is no CL.map or F.map that
can be used in the docking step. Can anybody help me solve this problem?
Thanks
>
> Haipeng Hu
>
> ________________________________________________
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>


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