Re: [AMBER] reasonable GIST griddim values

From: Daniel Roe <>
Date: Mon, 25 Oct 2021 10:38:11 -0400


So I didn't write that tutorial, but it sounds like it tries to find
grid dimensions for a 0.5 Ang. spacing. So the dimensions you got are
larger since presumably your system is larger than the tutorial
system. The issue you may run into is that 750^3 voxels will require
about 1.6 GB per grid (of which GIST uses several) so you might run
out of memory. If that's the case, you may want to try and focus on
particular regions of your solute.


On Sun, Oct 24, 2021 at 4:28 PM Christian Seitz <> wrote:
> Hello,
> I am learning GIST. In the GIST tutorial (
> there is a
> script ( to calculate griddim, the grid increments for the
> GIST calculation. The default values are (40,40,40) and the example values
> are similar. When I run the script, my griddim values are closer to
> (750,750,750). Is it reasonable to run GIST with such increments? If not,
> what values should I use instead? I am using crystal structures 5FRO and
> 6PUZ. These are crystal structures of a protein with DNA and a complexed
> ligand, with the goal of examining water in the ligand binding site. Thanks
> for your help!
> --
> *Christian Seitz*
> PhD Candidate, Biochemistry & Biophysics | UC-San Diego
> NSF GRFP Fellow, Amgen Scholar
> McCammon lab <> and Amaro lab
> <>
> <>
> [image:]
> <>
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Received on Mon Oct 25 2021 - 08:00:03 PDT
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