Re: [AMBER] short bonds in average pdb

From: Jason Swails <>
Date: Thu, 18 Oct 2012 09:44:31 -0400

On Thu, Oct 18, 2012 at 5:40 AM, Mu Xia <> wrote:

> 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.

This makes sense. H atoms typically rotate fairly freely (they are small
and there is little steric hindrance in many instances to free rotation).
Also, for groups like CH3, the 3 hydrogens are, at least approximately,
rotationally degenerate, meaning they should have approximately the same
average location (which will be nearly on top of the heteroatom).

> My question is, how could I get a correct average structure containing
> normal bonds and coordinates?

What you got *is* a correct average structure (i.e., it is *the* average
structure). "Normal bonds and coordinates" would be something you would
find in a 'representative structure' in cluster analysis or something of
the like.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Thu Oct 18 2012 - 07:00:05 PDT
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