AMBER Archive (2008)

Subject: Re: AMBER: artifacts in ptraj avg output

From: stephane acoca (stephane.acoca_at_gmail.com)
Date: Sat Apr 05 2008 - 04:52:26 CDT

Thank you, this "trick" worked really well :)

On Sat, Apr 5, 2008 at 5:11 AM, Barbault Florent <
florent.barbault_at_paris7.jussieu.fr> wrote:

> 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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