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

William Joseph Allen william.joseph.allen at gmail.com
Thu May 29 07:25:45 PDT 2014


Hi Yunierkis and Trent -

I thought I would jump in here for a quick comment. You may want to
double-check that you remembered to add partial charges to both the ligand
and receptor prior to generating grids / docking. Neglecting either of
those will always result in null electrostatic energy scores.

In the class we teach at Stony Brook, many of the students have this exact
same problem with electrostatic energies. 99% of the time, they forgot to
add partial charges to something.

Joe Allen


On Wed, May 28, 2014 at 10:05 AM, Trent E. Balius <tbalius at aol.com> wrote:

> 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:
>
> $DOCK_PATH/install/test/chemgrid_score/
>
> 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
>
> ======================================
> 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
>
>
> 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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> Fundada el 30 de noviembre de 1952. Visítenos en: http://www.uclv.edu.cu
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>
>
>
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-- 
William Joseph Allen, Ph.D.
Postdoctoral Associate
Dept. of Applied Mathematics and Statistics
Stony Brook University
http://ringo.ams.sunysb.edu/~wjallen/
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