[Dock-fans] parameters

Scott Brozell sbrozell at rci.rutgers.edu
Mon Jan 24 10:18:16 PST 2011


Hi,

Francesco, i have included the chimera list.
I have searched that list and did not find a bug report from you.
Can you confirm that it is a chimera bug and report the details ?

thanks,
scott

On Tue, Jan 18, 2011 at 08:53:28AM +0100, Francesco Pietra wrote:
> That about the vdw parameters was a wrong message by dock6.4.
> Actually. it was the format. To fit the MW code, the correct format is
> (i.e., C.3, H, etc). The one I got from dockprep in latest version of
> chimera was no good (c3, hc ...)
>
> @<TRIPOS>ATOM
>      1 C           2.5960   -1.2050    1.7710 C.3       1 A31   -0.0961
>      2 H           2.6980   -1.2650    0.6640 H         1 A31    0.0407
>

On Mon, Jan 17, 2011 at 10:04:57PM +0100, Francesco Pietra wrote:
> I have not been using dock6 for quite a time and now I am getting confused.
> 
> With dock6.4, anchor_and_grow, a mol2 file for the ligand, a grid,
> selected spheres for the receptor, and parameters:
> 
> vdw_defn_file        /usr/local/dock6/parameters/vdw_AMBER_parm99.defn
> flex_defn_file        /usr/local/dock6/parameters/flex.defn
> flex_drive_file       /usr/local/dock6/parameters
> 
> the out file:
> 
> .................
> .................
> Initializing Library File Routines...
> Initializing Orienting Routines...
> Read in 3000 spheres for orienting.
> Initializing Conformer Generator Routines...
> Initializing Grid Score Routines...
>  Reading the energy grid from /........../grid.nrg
>  Done reading the energy grid.
> WARNING assign_vdw_labels: No vdw parameters for 0  c3
> WARNING assign_vdw_labels: No vdw parameters for 1  hc
> WARNING assign_vdw_labels: No vdw parameters for 2  hc
> ...............................
> ...............................
> 
> My confusion is about these not found vdw parameters ("c" should be
> compatible with "C".. etc), while parameter location on the .in file
> is correct;
> 
> 
> francesco at tya64:/usr/local/dock6/parameters$ ls
> 1               leap                     screen.para
> antechamber     na.table.ambcrg          vdw_AMBER_parm94.defn
> chem.defn       prot.table.ambcrg.ambH   vdw_AMBER_parm96.defn
> chemgrid        prot.table.ambcrg.pdb3H  vdw_AMBER_parm99.defn
> chem_match.tbl  prot.table.ambcrg.pdbH   vdw.parms.amb
> flex.defn       prot.table.ambcrg.sybH
> flex_drive.tbl  screen.in
> francesco at tya64:/usr/local/dock6/parameters$
> 
> 
> 
> Also, the mol2 file (AM1 charges from antechamber) for the ligand looks like ok:
> 
> @<TRIPOS>MOLECULE
> A31.pdb
> 61 65 1 0 0
> SMALL
> AMBER ff99SB
> 
> 
> @<TRIPOS>ATOM
>       1 C           2.5960   -1.2050    1.7710 c3        1 A31   -0.0961
>       2 H           2.6980   -1.2650    0.6640 hc        1 A31    0.0407
>       3 H           2.5570   -2.2590    2.1300 hc        1 A31    0.0357
>       4 H           1.6160   -0.7340    2.0130 hc        1 A31    0.0297
> ...............................
> ...............................
> 


More information about the Dock-fans mailing list