Dear Amber community,
I have been using the following cpptraj input to obtain dx files for
visualizing the spatial distribution of water around a protein:
parm ../../production/100ns_1/FFFF_TTr1.prmtop
trajin ../../production/100ns_1/FFFF_TTr1_100ns_1.nc
autoimage anchor :27-29,47-49,67-69,87-89.CA,C,O,N origin
principal :27-29,47-49,67-69,87-89.CA,C,O,N dorotation
rms first :27-29,47-49,67-69,87-89.CA,C,O,N
average avg.pdb :1-120
grid FFFF_TTr1_100ns_1_242K_sdfOw-v1.dx 24 0.5 40 0.5 54 0.5 (:WAT.O)
run
Just want to check if I'm understanding the output correctly: The number
for each voxel is the number of frames in which that voxel was occupied by
a water oxygen, right?
Thanks!
Cianna
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Received on Thu Dec 26 2024 - 13:00:02 PST
