Is MD needed？

[lingling8023]

Which is the true "protein.nc" file?
In the quick tutorial, I have run the command "wk_minimize_trajectory.py -p protein_system.prmtop -t protein_system.nc -o protein_min.nc".
Next, I'm trying to run GIST analysis but want to know how to obtain the "protein.nc" file. Does this mean that I need to perform Molecular Dynamics simulation (e.g. Amber) to get it?
if I need to peform MD,where can I obtain setting files?

[lingling8023]

Besides,I try to use "protein_min.nc" as "protein.nc" and run "cpptraj -i gist.inp",find all numbers of output files(e.g. gist-dTStrans-dens.dx gist-gO.dx) are zero.
Hope you give me some advices.

Here is my command and gist.inp:
wk_prepare_receptor.py -i protein.pdb -o protein_prepared --pdb --amber_pdbqt
mkdir traj
run_waterkit.py -i protein_prepared_amber.pdbqt -c -67.378 -30.375 15.393 -s 20 20 20 -n 10000 -j 16 -o traj
wk_make_trajectory.py -r protein_prepared.pdb -w traj -o protein
wk_minimize_trajectory.py -p protein_system.prmtop -t protein_system.nc -o protein_min.nc
cpptraj -i gist.inp

"gist.inp"
parm protein_system.prmtop
trajin protein.nc
gist gridspacn 0.5 gridcntr 67.378 -30.375 15.393 griddim 40 40 40
go
quit