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

Dwight McGee dwight.mcgee at gmail.com
Sat Dec 3 17:50:36 PST 2016


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.
>
> Thanks!
>> Gustavo Seabra.
>
>
>
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>



-- 
T. Dwight McGee Jr.

dwight.mcgee at gmail.com

"Problems cannot be solved at the same level of awareness that created
them."
                Albert Einstein
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