Hello I'm trying to calculate the free energy of PDB file, with something like:
title "calculate free energy"
start FreeMD
prepare
print high
system gibbs_free
source model11.pdb
new_top new_seq
new_rst
center
orient
solvate box 10.0 20.0 30.0
free
update lists
end
task prepare
md
system gibbs_free
sd 100
end
task md optimize
task shell "cp gibbs_free.qrs gibbs_free.rst"
md
system gibbs_md
reference gibbs_free.qrs
noshake solute
print energies
end
task md energy
The error is "0: Failed to allocate scratch array smr4", a version without copying the rst file "could not open rst file". Would you give me some pointers on how to calculate the free energy of a protein.
Thanks
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