[AMBER] reasonable GIST griddim values

From: Christian Seitz <cseitz.ucsd.edu>
Date: Sun, 24 Oct 2021 13:27:07 -0700


I am learning GIST. In the GIST tutorial (
http://ambermd.org/tutorials/advanced/tutorial25/section3.htm) there is a
script (FindCentroid.py) 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 <https://mccammon.ucsd.edu/> and Amaro lab
cseitz.ucsd.edu <cseitz.elon.edu>
[image: www.linkedin.com/in/christianseitz21]
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Received on Sun Oct 24 2021 - 13:30:03 PDT
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