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

From: He, Amy <>
Date: Thu, 25 Mar 2021 04:59:06 +0000

Hi Dr. Giambasu,

Thank you so much for your kind advice. It was really helpful! And I was able to get smaller blobs using the higher threshold values as you suggested.
I built the protein from a crystal structure, so I align the positions given from MoFT with the crystal structure. I am able to trim down a lot of points when threshold varies from 0.1 to 0.3, and the alignment is still great with the crystallographically-resolved water molecules.

I have two more questions about choosing a threshold value and about the occupancy values:
(1) As the threshold increases, more and more points are eliminated, because the Laplacian at these positions is less negative than the reference Laplacian (=threshold*min(Laplacian)). Is it right to think that the eliminated positions are likely the false positives where a solvent molecule should not be placed at?
(2) For the occupancy values, am I right in thinking that one can average the occupancy values by volume of the blob, or is there some way to get the individual occupancy value for each position in a blob?

Thank you again for your time and kind help.

Amy H

Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
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Received on Wed Mar 24 2021 - 22:00:02 PDT
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