ADL: regarding active site

Davide Mercadante dmer018 at aucklanduni.ac.nz
Mon Jun 15 02:36:36 PDT 2009


Dear kaustubh,

Thanks for posting your case. It is exactly what happens to me with my
system...

Hope we will find a solution soon to the problem...
I am out of the university at the moment for a conference, but as soon as
possible I will have access to my file I will post them as well...

Cheers,
Davide

2009/6/15 kaustubh <kaustubh.joshi at systemsbiology.fi>

>
> 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
> >> Sent from the AutoDock mailing list archive at Nabble.com.
> >>
> >> ________________________________________________
> >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list---
> >>
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> >
>
> --
> View this message in context:
> http://n2.nabble.com/regarding-active-site-tp3066853p3079355.html
> Sent from the AutoDock mailing list archive at Nabble.com.
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


More information about the autodock mailing list