I solved it, many many thanks for your help!
On Tue, Jul 25, 2017 at 12:10 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Aligned to what? RMSD allows you to align to a given set of coords.
>
> Bill
>
>
> On 7/24/17 5:56 PM, Elisa Pieri wrote:
> > 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 - 15:30:06 PDT
