Hi all,
I want to get an average structure of the ligand-protein complex from the trajectories generated by MD. So I use the ptraj command. The input file is as following.
trajin production1.mdcrd
rms first mass .CA,C,N
average a.pdb pdb
When examining a.pdb in VMD, I find that the X-H (X is the heavy atom) bonds are abnormally short.
My question is, how could I get a correct average structure containing normal bonds and coordinates?
Many thanks!
Mu Xia,
Zhejiang University, China
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Received on Thu Oct 18 2012 - 03:00:03 PDT
