ADL: regarding active site

kaustubh kaustubh.joshi at systemsbiology.fi
Mon Jun 15 02:27:51 PDT 2009


Yes I am using autogrid4
and here are the details of gpf file:

I centered it on the on the ethereal oxygen present in the native molecule
GWE999 of 3DM2.pdb

npts 60 60 60                        # num.grid points in xyz
gridfld 3DM2M.maps.fld               # grid_data_file
spacing 0.375                        # spacing(A)
receptor_types A C H HD N NA OA SA   # receptor atom types
ligand_types A C S F CL BR P HD N NA OA SA # ligand atom types
receptor 3DM2M.pdbqt                 # macromolecule
gridcenter -3.227 -33.066 21.673   # xyz-coordinates or auto
smooth 0.5                           # store minimum energy w/in rad(A)
map 3DM2M.A.map                      # atom-specific affinity map
map 3DM2M.C.map                      # atom-specific affinity map
map 3DM2M.S.map                      # atom-specific affinity map
map 3DM2M.F.map                      # atom-specific affinity map
map 3DM2M.CL.map                     # atom-specific affinity map
map 3DM2M.BR.map                     # atom-specific affinity map
map 3DM2M.P.map                      # atom-specific affinity map
map 3DM2M.HD.map                     # atom-specific affinity map
map 3DM2M.N.map                      # atom-specific affinity map
map 3DM2M.NA.map                     # atom-specific affinity map
map 3DM2M.OA.map                     # atom-specific affinity map
map 3DM2M.SA.map                     # atom-specific affinity map
elecmap 3DM2M.e.map                  # electrostatic potential map
dsolvmap 3DM2M.d.map              # desolvation potential map
dielectric -0.1465                   # <0, AD4 distance-dep.diel;>0,
constant






bagdevi wrote:
> 
> Can you locate 3DM2.gpf in your working directory. Your details
> regarding grid must be specified in it. And are you running autogrid4
> using this gpf file.
> 
> 
> Regards,
> Bagdevi Mishra.
> 
> 
> 
> 
> On Mon, Jun 15, 2009 at 12:40 PM,
> kaustubh<kaustubh.joshi at systemsbiology.fi> wrote:
>>
>>
>> Dear Stefano, Bagdevi,
>>                                   I did tried to follow your
>> instructions,
>> but in all the cases i failed totally. Main problem I found is the grid
>> is
>> not generated at the point I am specifying.
>> For example I am attaching a protein structure and a ligand.
>> For this system, the active site includes residues 100, 103, 105,
>> 179,181,
>> 188,190, 227.
>> I tried by different ways to assign the grid occupying all these
>> residues,
>> but none of the methods worked. Instead the grid generation and docking
>> respectively take place at another position (viz. residues
>> 332,419,420,421)
>> which are located at the surface of protein and quite distinct from the
>> expected active site.
>> Could some body try a quick run on this system and explain with method
>> followed how to approach right docking.
>>
>>
>> Thanks in advance
>>
>> Kaustubh
>>
>>
>> http://n2.nabble.com/file/n3078883/3DM2.pdb 3DM2.pdb
>> http://n2.nabble.com/file/n3078883/8.pdbqt 8.pdbqt
>> --
>> View this message in context:
>> http://n2.nabble.com/regarding-active-site-tp3066853p3078883.html
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>>
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>>
> ________________________________________________
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> 

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