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AMBER Archive (2009)Subject: [AMBER] Average structure over simulation
From: Olotu Odunayo (paxoo_at_nottingham.ac.uk)
Hi,
i'm using this ptraj input file to get an average structure over a period of simulation, some of the residues of my protein looks sewn together
trajin Equil.mdcrd
ptraj ddd.prmtop < ptraj.in
but if I create a pdb file from the .rst file, individually e.g below, it looks just fine
ambpdb -p ddd.prmtop < Md.rst > Md.pdb
Just want to check if this happens sometimes!
Thanks
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