[AMBER] Mask behavior vs distance measurement?

From: Kenneth Huang <kennethneltharion.gmail.com>
Date: Thu, 9 Jul 2020 20:04:10 -0400

Hi all,

I'm running into an odd situation where the behavior of the mask command
doesn't seem to be lining up exactly with the actual measured distance, ie
if I have

mask "(:35.N4<:5.5)&:47-135&( :LYS.NZ | :ARG.NH1,NH2 | :GLU.OE1,OE2 |
> :ASP.OD1,OD2 )" maskout maskout_N4.dat

To measure any charged groups of the protein within 5.5 A of the N4 group
on a DNA base, it says frame 1 has both NH groups on an ARG within the

#Frame AtomNum Atom ResNum Res MolNum
> 1 2527 NH1 108 ARG 3
> 1 2530 NH2 108 ARG 3

But when I try to fetch the distance via

distance dN4 :35.N4 :108.NH1 out dist.m35N4-108.dat noimage
> distance dN4b :35.N4 :108.NH2 out dist.m35N4b-108.dat noimage

The distance I get for both sets say that it's mugh further than the 5.5
radius of mask?

       1 6.4996
       1 5.7482
My first thought is I've somehow messed up the selection algebra in the
mask portion, but I can't seem to find an actual error in it?



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Received on Thu Jul 09 2020 - 17:30:03 PDT
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