On Tue, Aug 28, 2012 at 10:05 AM, Sanjib Paul <sanjib88paul.gmail.com>wrote:
> Dear Amber Users,
> I wanted to generate a average structure form 1
> ns trajectory file of my protein using 'average' command of ptraj. My input
> file is like following:
> trajin protein_prod_1ns.mdcrd
> average protein_prod_1ns_avg.pdb pdb
>
Note, the 'average' command does not do any kind of implicit fitting, so
you are including free rotation and translation in your average (which is
*NOT* something you probably want to do).
To get rid of these contributions, add a "rms" command before 'average'.
> When I observe my pdb file of average structure I noticed that some portion
> of protein is very unstable and very absurd. Atoms are overlapping and some
> unusual bonds are also present. Then, I followed analysis portion of
> TUTORIAL B3. Here also structure is like before. Some unusual bonds and
> overlapped atoms are present. How can I overcome it? Please help.
>
'Warped' and 'strange' structures are expected for an average (to some
extent). Consider for instance a freely rotating methyl group such that
all hydrogens attached to the CH3 are rotationally degenerate. In this
case, each hydrogen atom should have the *same* average coordinates which
should lie almost directly on top of the C atom they are all attached to.
You should think about what you really want and whether or not an 'average'
structure satisfies your needs.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Aug 28 2012 - 07:30:04 PDT
