Re: [AMBER] 3D-RISM solvent placement with MoFT

From: George M. Giambasu <>
Date: Tue, 23 Mar 2021 21:31:53 -0400

Hi Amy - thanks for reporting your analysis.

I wonder how the occupancy values look when you use a threshold of say
0.5. Doing so will "shrink" the Laplacian blobs and will avoid
integrating the density over delocalized blobs.

It takes a little experimentation to find the right values for the
threshold and one way to do so is to open the Laplacian maps in chimera,
vmd or pymol and see at which negative isovalue the Laplacian blobs
start to look more "localized". When run using the --blobs, or
--blobsper options metatwist reports the ranges of Laplacian values used
to map water binding modes so you can double check.

Let us know how this worked for you,

George Giambasu.

AMBER mailing list
Received on Tue Mar 23 2021 - 19:00:02 PDT
Custom Search