Hi all,
I looked at the previous thread
http://archive.ambermd.org/201202/0617.htmland got the ptraj strip
code to
use.
strip !(:1-107<.6.0)
So I have made these lines for testing
trajin test_md2.mdcrd
strip !(:1-11<5.0)
trajout pdb/test-edited.pdb pdb dumpq
my test peptide has 11 residues. However, the results shows me that non of
the water is stripped from the original structure. I also have tested with
loading just one pdb file which has water molecules that are very far away(
more than 10A) and still did not work.
I am currently working on AMBER 11 and any help will be greatly
appreciated.
Kim
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Received on Thu Feb 07 2013 - 16:30:03 PST
