Sorry, maybe I didn't make my question very understandable :)
I would like to get a new nc file where the protein is aligned in each
frame as an output. Can RMSD do this? From the manual,it doesn't seem so.
Elisa
On Mon, Jul 24, 2017 at 11:09 PM, Xing <stecue.gmail.com> wrote:
> Dear Elisa,
>
> Sorry if I misunderstand the question...I don't know the details of REMD,
> but why couldn't we just use the "rmsd" command in cpptraj? It has a
> "previous" option to align current frame to its previous
> frame, or whatever frame if using "ref #" according to the manual.
>
> Thanks and best wishes,
> Xing
>
> On 07/24/2017 03:59 PM, Elisa Pieri wrote:
> > Hello,
> >
> > I have a curiosity: I have a nc trajectory obtained from REMD, so the
> > frames are actually not-consecutive snapshots. Is there a tool to align
> the
> > protein from frame to frame?
> >
> > I'm performing cluster analysis on it, and would like to be sure that
> this
> > issue is not a problem in calculating RMS and average structures. Right
> > now, average structures are completely unrealistic.
> >
> > Suggestions?
> >
> > Elisa
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Received on Mon Jul 24 2017 - 15:00:02 PDT
