[AMBER] cpptraj grid output

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 12 Oct 2016 17:39:01 +0200

I’m trying to work out the water density around two ligands bound to a protein. I’m using cpptraj grid in conjunction with the bounds command.
I’m using the following script

# the mask refers to the two ligands

parm myprt_solv.prmtop
train mytraj_100ns.nc
rms first :126-127&!.H= mass
bounds :126-127 dx .5 name MyGrid out bounds.dat
average bounds.mol2 :126-127
createcrd MyCoords
crdaction MyCoords grid bounds.xplor data MyGrid :WAT.O

I obtained a bounds.xplor file with the following warnings
CTION SETUP FOR PARM '3n7h_de4_solv.prmtop' (5 actions):
  0: [autoimage]
        Original box is truncated octahedron, turning on 'familiar'.
        Anchor molecule is 1
        The following molecules are fixed to anchor: 2 3
        3738 molecules are mobile.
  1: [rms first :126-127&!.H= mass]
        Target mask: [:126-127&!.H*](28)
        Reference mask: [:126-127&!.H*](28)
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning: after the RMS-fit is performed.

My question are (a) whether autoimage is needed and (b) does the .xplor file relate to the protein coordinates of the first frame of the trajectory?

Thanks in advance for any clarifications/suggestions


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Received on Wed Oct 12 2016 - 09:00:03 PDT
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