[Dock-fans] dock6.6 and dock3.5 scoring
yunierkis at uclv.edu.cu
Fri May 16 07:15:02 PDT 2014
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:
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
Universidad Central "Marta Abreu" de Las Villas.
Fundada el 30 de noviembre de 1952. Visítenos en: http://www.uclv.edu.cu
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Dock-fans