> there appears to be trouble with duplicate atom names.
Since you simulated the dimer itself already, the dimer itself is
presumably not the problem, just the 'big' pdb file. To manually perform
the same check as leap, you could try something like this:
$ awk '{print $1,$2,$3}' big.pdb | sort | uniq -c | awk '$1 > 1'
where instead of the first $1,$2,$3 you use the actual field numbers
for residue number, res name, and atom name (counting from 1). This
should just confirm the duplicates that leap is seeing, pointing to
what needs fixing.
Bill
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Received on Tue Nov 08 2011 - 09:00:05 PST
