After molecular mechanics optimization, I could not get optimized coordinate PDB file. The "1IVD_opt_final_1.pdb" was the same as the "1IVD_opt.pdb" file. How can I get the final optimized coordinate PDB file?
The prepare file is as follow:
start 1IVD
permanent_dir ./perm
scratch_dir ./data
prepare
system 1IVD_opt
source 6.pdb
periodic
new_top new_seq
new_rst
center
orient
solvate box 8.0
modify segment 471 quantum
update lists
ignore
write 1IVD_opt.pdb
write 1IVD_opt.rst
end
task prepare
The MM optimization input file is as follow:
echo
start 1IVD
memory total 25000 Mb
permanent_dir ./perm
scratch_dir ./data
prepare
read 1IVD_opt.rst
write 1IVD_opt_mm_1.rst
end
task prepare
md
system 1IVD_opt
sd 2000 init 0.01 min 1.0e-5 max 0.05
noshake solute
msa 6000
record rest 1
record coord 1
print step 1 extra
print energies 1
end
task md optimize
prepare
read 1IVD_opt.rst
write 1IVD_opt_final_1.pdb
end
task prepare
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