[AMBER] short bonds in average pdb

From: Mu Xia <muxiachuixue.163.com>
Date: Thu, 18 Oct 2012 17:40:34 +0800 (CST)

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
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