| 5:28:05 AM PDT - Thu, Aug 25th 2011 |
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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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