[Dock-fans] WARNING assign_vdw_labels: No vdw parameters for 0 BR.3

Scott Brozell sbrozell at rci.rutgers.edu
Thu Jul 30 15:28:19 PDT 2009


Hi,

On Tue, Jul 28, 2009 at 02:50:09PM +0530, gomathy ramanathan wrote:
> I tried to run a ligand.mol2 file against a protein , which gave me a
> dock score of -23/ But it says ""Initializing Library File Routines...
> Initializing Orienting Routines...
> Initializing Grid Score Routines...
>  Reading the energy grid from grid.nrg
> WARNING assign_vdw_labels: No vdw parameters for 0  BR.3
> 
> -----------------------------------
> Molecule:                DRG
> 
>  Elapsed time:  14 seconds
> 
>  Anchors:               1
>  Orientations:          500
>  Conformations:         500
> 
>  Grid Score:          -23.012138
>          vdw:          -18.583191
>           es:           -4.428946
> But when i checked the vanderwalls parameter file99,the bromine was
> also defined.
> I have also attached my ligand.mol2 file. Could u plz let me know why
> is this error .

In DOCK Sybyl atom types are case sensitive.
http://tripos.com/mol2/atom_types.html
Bromine is Br

This works for me:

@<TRIPOS>ATOM
     1  BRAC        0.510     6.400     0.010   Br.3      1 DRG       0.016
     2  CAG         1.720     4.940     0.010   C.ar      1 DRG       0.003
     3  CAE         1.320     3.670     0.020   C.ar      1 DRG      -0.018
     4  CAH         2.420     2.920     0.020   C.ar      1 DRG       0.292
     5  OAA         2.420     1.690     0.030   O.2       1 DRG      -0.680
     6  OAF         3.550     3.680     0.010   O.ar      1 DRG       0.200
     7  CAI         3.110     4.980     0.000   C.ar      1 DRG       0.155
     8  CAD         3.930     6.110    -0.010   C.2       1 DRG       0.016
     9  BRAB        5.800     6.010    -0.020   Br.3      1 DRG       0.016
    10  H001        0.375     3.343     0.026   H         1 DRG       0.000
    11  H002        3.500     7.013    -0.012   H         1 DRG       0.000

Scott



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