Dear AMBER members,
I tried ptraj trajout script in amber tools 10 for a peptide in water.
The problem is that the structure of the peptide is
different (showing turn
in contrast to alpha-helix) after the script is run. Note that, the
residue numbers
for the peptide is 1 to 25 and the system contains a Na+ ion (residue
number 26).
Script:
.........................................................
trajin p1.mdcrd
trajin p2.mdcrd
trajout all.mdcrd
center origin :1-25
image origin center familiar
........................................................
Command:
ptraj <original prmtop file> <ptraj script>
Anything wrong with this? Am I forgetting to do something here?
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Received on Mon Nov 19 2012 - 00:00:02 PST
