Re: [AMBER] question about GIST calculation

From: Steven Ramsey <>
Date: Tue, 30 Jul 2019 10:39:01 -0400


Yeah that python script was written to simply suggest a grid centroid for
the gist calculations. It is not necessary to complete the tutorial but may
be helpful for defining grids without visualization.

Using visualization instead of the script you could load your structure
into vmd, pymol, or tools like autodock vina to visualize the binding site
of interest and choose where to place the center of your GIST grid.
(Docking visualizations are particularly good since they will often render
a gridded region for you to see which should match the GIST grid)

The script was written in python 2 so if you are using python 3 to run it
that is probably the root of the issue. If you want help to troubleshoot
that script I'd be happy to help, but I will need to see the inputs to be
more helpful.

Hope this helps,


On Tue, Jul 30, 2019 at 6:17 AM Aliakbartehrani Zahra <> wrote:

> Dear all,
> I am testing GIST calculation in my system by following this tutorial
> and it has been failed when I have used “helper script” for making
> recommended gist input commands. So I am wondering its universal script or
> should be changed. I have used it on my ligand-bound pdb structure with the
> same name used (4QC) in the tutorial but got the following error. Any
> suggestion/help would be appreciated.
> ['4QC']
> Traceback (most recent call last):
> File "", line 207, in <module>
> parseData(line)
> File "", line 126, in parseData
> ATOM.append(Atom(name,idnum,char,tp,att1,att2,x,y,z,av,bv,n,line))
> File "", line 74, in __init__
> Self.point = Point(float(x),float(y),float(z))
> ValueError: invalid literal for float(): -4.180 12
> Bests
> Zahra
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Received on Tue Jul 30 2019 - 08:00:02 PDT
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