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 Sun Mar 21 2021 - 19:30:02 PDT
