[Dock-fans] parameters

Francesco Pietra chiendarret at gmail.com
Mon Jan 17 13:04:57 PST 2011


Hello:
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
...............................
...............................



Thanks for help
francesco pietra


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