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

Trent E. Balius tbalius at aol.com
Wed May 28 07:05:19 PDT 2014

Hi Yunierkis,

It looks like from your error message that there is a problem reading 
in the
solvmap grid.  Was this generated correctly?

That is weird that you are get electrostatics energies of zero.  This 
implies that there is an issue with your electrostatic grids; probably, 
the error occurs when the delphi grid is converted (grid-convrds, your 
step 7).

the dock3.5 score is evaluated in the following test directory:


Are your electrostatic components  zero for all tests (dockout files)?

Does chemgrid4.dockin run.  This test includes the ligand desolvation?

Note that I was able to run these tests using DelPhi V. 5.1

I hope that this helps,


Trent E. Balius, PhD
Shoichet Lab – Faculty of Pharmacy,
University of Toronto
Office Phone: (416) 946-7304
Cell Phone: (516) 381-0926
URL: http://docking.org/~tbalius

---- Original Message ----
From: yunierkis <yunierkis at uclv.edu.cu>
To: dock-fans <dock-fans at docking.org>
Sent: Fri, May 16, 2014 10:06 am
Subject: [Dock-fans] dock6.6 and dock3.5 scoring


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

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

dock3.5_electrostatic_score                                  yes
dock3.5_ligand_internal_energy                               no
dock3.5_ligand_desolvation_score                             volume
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

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

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