[Dock-fans] GRID reading the wrong atom type?

Scott Brozell sbrozell at rci.rutgers.edu
Sun Dec 4 16:25:19 PST 2016


Hi,

I reproduced the issue on Friday and noted that changing copper to zinc
in the pdb file showed similar behavior, so this appears to be a grid
program issue.

It would be nice to hear from someone that has actually used the
Hawkins gbsa score.  

scott

On Sat, Dec 03, 2016 at 08:50:36PM -0500, Dwight McGee wrote:
> Hi Gustavo,
> 
> Are you still having an issue with this? I have not had time yet to
> thoroughly go through the code but at first glance your implementation
> seems to be correct and I think the code would have outputted and error if
> anything was missing or inappropriately labelled.
> 
> I will continue to investigate and report back soon.
> 
> Best,
> Dwight
> 
> On Thu, Dec 1, 2016 at 12:39 AM, Gustavo Seabra <gustavo.seabra at gmail.com>
> wrote:
> 
> > Dear all,
> >
> > I???m having an issue when generating a grid for a target that has Copper
> > ions on it, and I???d really appreciate some help pinpointing the problem.
> >
> > I have an enzyme that contains 2 copper ions in the active site. The mol2
> > file for it is here:
> >
> >   https://www.dropbox.com/s/ot91h7wkisojowp/PPO3_with_charges.mol2?dl=0
> >
> > I have modified the vdw_AMBER_parm99.defn file to contain the Copper
> > parameters, by including the following lines in it, right after the Zn2+
> > definition:
> >
> > name            Copper
> > atom_model      all
> > radius          1.218
> > well_depth      0.00148497
> > heavy_flag      1
> > valence         8
> > gbradii         1.39
> > gbscale         0.80
> >
> > definition      Cu
> > _____________________________________
> >
> > (I am trying to use the parameters from Li et al, JCTC 2013, 9, 2733)
> >
> > The modified file is here:
> >
> >   https://www.dropbox.com/s/8tyx1a39jx45pya/vdw_AMBER_parm99.defn?dl=0
> >
> > Finally, I try running GRID ( $ grid -i grid.in -o grid.out -v) with the
> > grid.in file as here:
> >
> >   https://www.dropbox.com/s/jc0dpuqkoy3qm7l/grid.in?dl=0
> >
> > Grid does run normally, with no error messages. HOWEVER, looking inside
> > the grid.out file, I get these lines:
> >
> >   6232   CU    Cu Carbon               1 19
> >   6233   CU    Cu Carbon               1 19
> >
> > I took the liberty to look into the code (label_vdw.c), and those lines
> > seem to be printed by the command below:
> >
> >     for (i = 0; i < molecule->total.atoms; i++)
> >       fprintf (global.outfile, "%6d %4s %5s %-20s %d %d\n", i + 1,
> >         molecule->atom[i].name,
> >         molecule->atom[i].type,
> >         label_vdw->member[molecule->atom[i].vdw_id].name,
> >         molecule->atom[i].heavy_flag,
> >         label_vdw->member[molecule->atom[i].vdw_id].bump_id);
> >     fprintf (global.outfile, "\n\n???);
> >
> >
> >
> > So, it seems to me that grid is assigning the CARBON vdW definitions to
> > Copper atoms. Is this correct? How can I check that GRID is using the
> > correct parameters for my copper atoms?
> >
> > Or, if it is really using the wrong parameters, how can I make GRID use
> > the correct parameters?
> >
> > I really appreciate any help you can give me here.


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