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You are welcome. Yes, you can simply redirect the output to a new file
}
' file.pdb file.pdb > new_file.pdb

Otherwise, I am not sure if I understand what you mean. The awk script itself was...

Hi, try:
awk '
NR==FNR {
if($3=="CA")
A[$6]=substr($0,61,6)
next
}
{
print substr($0,1,66) A[$6] substr($0,73)
}
' file.pdb file.pdb

--
Note: the file needs...

Try:
sed '/^ATOM /s/./A/22' file

a little bit verbose with some assumptions based on a sample, but....
awk -f egy.awk Mymulti-mol2File where egy.awk is:

BEGIN {
if (!grid) grid=-30.0000
}
/Name:/ {flag=0;block=$0;next}...