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

From: He, Amy <he.1768.buckeyemail.osu.edu>
Date: Mon, 22 Mar 2021 17:32:12 +0000

Hi again,


I read the log (.blobs) file produced by the command and I think I understand a little bit more. This is what I found in the .blobs file:

# Blob - index
# Max[x,y,z] - coordinates of the point where density is maximum within the blob.
# Occ[#] - integrated occupancy of the blob.
# V[A^3] - volume occupied by the blob.
# M[x,y,z] - average position (first moment) of the blob.
# Var[A^2] - average variance (second moment) of the blob.
# rave/max - ration between density at the average position and maximum value of density.
Blob Max[x,y,z] Occ[#] V[A^3] M[x,y,z] Var[A^2] rave/max[%]
    0 ( 97.780 57.122 36.531) 1073.278 16353.362 ( 44.732 41.949 46.326) 0.744 0.000
    0 ( 97.780 61.277 42.793) 1073.278 16353.362 ( 44.732 41.949 46.326) 0.684 0.000
    0 ( 98.126 67.162 40.706) 1073.278 16353.362 ( 44.732 41.949 46.326) 0.795 0.000
    0 ( 98.473 61.277 45.925) 1073.278 16353.362 ( 44.732 41.949 46.326) 0.604 0.000
    0 ( 98.820 51.929 46.272) 1073.278 16353.362 ( 44.732 41.949 46.326) 0.727 0.000
    0 ( 98.820 59.892 46.620) 1073.278 16353.362 ( 44.732 41.949 46.326) 0.586 0.000

Is the occupancy 1073.278 a sum of the occupancy values for the Max points in Blob #0? Is it normal to get such a huge blob #0 in Laplacian analysis, since the other blobs only contain one point each? If that is normal, is there any way to get the individual occupancy values for those Max points from the Laplacian analysis?


Many thanks,
Amy H

--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
he.1768.osu.edu
From: He, Amy <he.1768.buckeyemail.osu.edu>
Date: Sunday, March 21, 2021 at 10:10 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: 3D-RISM solvent placement with MoFT
Dear Amber Community,
I am using Amber 20 and I use 3D-RISM in sander to compute the solvent distribution for a single-frame protein structure. Then I use the 'metatwist' application in MoFT for water and ion placement by Laplacian analysis. The command I use to place the oxygen atoms of water molecules is:
metatwist --dx complex.kh.O.0.ccp4 \
--ldx convolution-complex.kh.O.ccp4 --map blobsper \
--species O WAT --bulk 55.55 --threshold 0.1 > complex.blobs
In the output complex.kh.O.0-convolution-complex.kh.O-blobs-centroid.pdb files, I get very high values in the 'occupancy' column (columns #55-60) for the first a few positions, please see a sample below:
ATOM      1   O  WAT C   1      97.780  57.122  36.5311073.28 31.44           O
TER
ATOM      2   O  WAT C   2      97.780  61.277  42.7931073.28 31.44           O
TER
ATOM      3   O  WAT C   3      98.126  67.162  40.7061073.28 31.44           O
TER
ATOM      4   O  WAT C   4      98.473  61.277  45.9251073.28 31.44           O
TER
ATOM      5   O  WAT C   5      98.820  51.929  46.2721073.28 31.44           O
TER
ATOM      6   O  WAT C   6      98.820  59.892  46.6201073.28 31.44           O
TER
I have the same issue with the blobs-centroid.pdb files that I get for ion placement. The coordinates seem fine. What am I doing wrong? How could I interpret the occupancy values?
Massive thanks,
Amy H
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Received on Mon Mar 22 2021 - 11:00:02 PDT