[Dock-fans] dock6.6 and dock3.5 scoring

yunierkis yunierkis at uclv.edu.cu
Fri May 16 07:15:02 PDT 2014


Hi

I've been trying the dock3.5 scoring feature withing dock6.6 and I've faced some problems. I'm following the examples provided with the dock 6.6 installation. In brief, these are the steps I followed to produce the necessary grid files

1) Generate a receptor pdb file containing only polar Hs (with chimera).
2) Rename all Hs to match the prot.table.ambcrg.ambH file definitions.
3) Run solvmap
4) Run solvgrid. For both solvmap and solvgrid I used a grid spacing of 0.25 A
5) Generate the selected spheres pdb file an merge with the receptor pdb file (rec+sph.crg)
6) Run delphi (v 6.2)
7) Run grid-convrds

Until here I got no error and all output files seems to be correctly created.

Then, I run dock6 with the following dock3.5 scoring specific settings:

dock3.5_grd_prefix                                           ../../grid3.5_v1/chem52
dock3.5_electrostatic_score                                  yes
dock3.5_ligand_internal_energy                               no
dock3.5_ligand_desolvation_score                             volume
dock3.5_solvent_occlusion_file                               ../../grid3.5_v1/solvmap
dock3.5_redistribute_positive_desolvation                    no

And I get the following error:

Reading chemgrids from ../../grid3.5_v1/chem52.cmg
Reading DelPhi grid from ../../grid3.5_v1/chem52.phi
Reading ligand desolvation grid from ../../grid3.5_v1/solvmap


Memory bounds exceeded for solvent occlusion grid. Program will terminate.

The examples provided with dock 6.6 installation seems to work fine but I think I'm also having some problems with the delphi grids.
In the case of the examples I always get 0.0 for electrostatic scores which should not be correct.
I'm able to load the electrostatic potential map generated with delphi in chimera and associate it with my receptor. However when I attempt to load the chem52.phi file into chimera, I got the error:

Error reading file chem52.phi, format delphi
Negative record size -1053817856


Have anyone experienced these issues with the dock3.5 score? How should I proceed to make dock3.5 scoring work?

Thanks in advance for any help

Yunierkis


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Universidad Central "Marta Abreu" de Las Villas.
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