[AMBER] autoimage for grid analysis with cpptraj

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Tue, 22 Sep 2020 10:05:57 +0000

I am trying to perform a grid analysis with a small peptide and a number of other molecules. I think managed to work out most of the details though one question remains.

I was recommended to use the “familiar” option with autoimage.

    autoimage :1-11 origin familiar
    rms rms_1-11_ds_of :1-11 out rms_1-11_out_of.dat first
    average avg1-11_of.pdb :1-11
    grid out_1-11_AAC_of.xplor 60 0.5 60 0.5 60 0.5 :AAC

However, I have run the same analysis without the “familiar” option and I cannot detect any difference at all. Is this familiar recommendation based on the old “image” methodology and can ignored now or should it indeed remain. Are there any benefits for using the familiar truncated-octahedral shape? The original cell is not a truncated octahedron.

Best regards
// Gustaf
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Received on Tue Sep 22 2020 - 03:30:02 PDT
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