Re: [AMBER] short bonds in average pdb

From: <>
Date: Thu, 18 Oct 2012 10:09:54 -0400 (EDT)

Hi Mu,

Jason is absolutely correct here, but for the sake of prettier
presentations, it is common to take the average structure that amber gives
you and conduct a short energy minimization of it. This should give you a
chemically normal-looking structure that is at least somewhat close to the
average one. Alternatively, you would pick and show the snapshot from your
MD that has the lowest rmsd compared to the average one. I find that to be
a good compromise between the true average and a model that people can
make sense of.


On Thu, October 18, 2012 9:44 am, Jason Swails wrote:
> 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.
> HTH,
> Jason
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list

Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Thu Oct 18 2012 - 07:30:02 PDT
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