metals with prepare

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Dear all,

I am a new user of Nwchem. I am using the Prepare module to built a system formed by a protein and a metal. The system is built correctly, but the metal is placed out of its binding site; instead it is located outside the protein. The input is like this:

prepare
source snap.pdb
new_top new_seq
new_rst
center
orient
solvate
update lists
ignore
write built.rst
write built.pdb
end
task prepare


Can someone explain why this displacement takes place? How can I avoid it?

Thanks in advance

Jon


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