AMBER Archive (2008)

Subject: Re: AMBER: artifacts in ptraj avg output

From: Barbault Florent (florent.barbault_at_paris7.jussieu.fr)
Date: Sat Apr 05 2008 - 04:11:37 CDT

Hi

Your protein is ok. In fact, the average command is just an arithmetic
operation then you have a cartesian average of whole atomic
coordinates. If you want to work with a representative structure, I
suggest you to calculate the RMSD versus time with this average
protein structure as reference. Thus, you just have to pick the
conformation with the lowest RMSD value, which is the conformation the
most closest to the average (and a "real" structure).

Hope this will help you.
Regards
Florent Barbault

On Sat, 5 Apr 2008 04:46:55 -0400
  "stephane acoca" <stephane.acoca_at_gmail.com> wrote:
> HI , I ran an MD and tried to output the average structure of the
>protein.
> When I do that, the protein seems to have numerous artifacts. I
>added the
> protein structure for you guys to see what i'm talking about.
> Thanks,
>
> Steve

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