I cant find any examples about what kind of files and how QMMM output files may converting in xtc format for Pymol.
After QMMM dynamics I havent trajectory files.
The Analize directive will not work with QMMM output files, because absent trj files after QMMM dynamics. Am I right?
How I may vizualize moleclar motion?
My prep.nw
start protein_dyn
prepare
source protein3_pdbset1.pdb
new_top new_seq
new_rst
modify segment 11 quantum
update lists
ignore
center
orient
solvate cube 6
write protein_dyn.rst
write protein_dyn.pdb
end
task prepare
My dynamics.nw
start protein_dyn
permanent_dir ./permanent_dir/dynamics
scratch_dir ./scratch_dir
md
system protein_dyn
data 50
isotherm
print step 1 stat 10
end
basis
* library "6-31G"
end
scf
vectors output TOP.movecs
print convergence information mulliken ao
maxiter 50
thresh 1.0e-4
end
qmmm
region qmlink
bqzone 2.0
ncycles 2
density espfit
xyz qw
end
task qmmm scf energy
task qmmm scf dynamics
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