Hi,
Everything seems ok, especially if the RMS values you are getting make
sense. The best way to make sure though is to write out the rotated
trajectory with a 'trajout' command and visualize it.
Hope this helps,
-Dan
On Wed, Jun 16, 2021 at 12:06 PM Martin Rosellen
<martinrosellen.googlemail.com> wrote:
>
> Sorry for that. Here is the cpptraj commands to calculate RMSD values of hairpins:
>
> parm native_hex.prmtop
> trajin native_hex.inpcrd
> trajin productions/prod_1.nc
>
> autoimage
> strip :WAT,Cl-
> strip .H*
>
> align :1-1332.CA&!:2-12,223-233,444-454,665-675,886-896,1107-1117
>
> rmsd :2-12.CA out body_aligned/rmsd_hairpin_1.dat nofit
>
> rmsd :223-233.CA out body_aligned/rmsd_hairpin_2.dat nofit
>
> rmsd :444-454.CA out body_aligned/rmsd_hairpin_3.dat nofit
>
> rmsd :665-675.CA out body_aligned/rmsd_hairpin_4.dat nofit
>
> rmsd :886-896.CA out body_aligned/rmsd_hairpin_5.dat nofit
>
> rmsd :1107-1117.CA out body_aligned/rmsd_hairpin_6.dat nofit
>
> It is clear to me now that if the hexamer would have been rotated for the best fit by the ‘align’ command then all the RMSD values of the hairpins would be really high. Still, is it possible that the hexamer is rotated by ‘align’ for the best fit?
>
> best
> Martin
>
>
>
>
> > On 16. Jun 2021, at 15:23, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > Hi,
> >
> > On Wed, Jun 16, 2021 at 8:55 AM David A Case <david.case.rutgers.edu> wrote:
> >>
> >> On Wed, Jun 16, 2021, Martin Rosellen wrote:
> >>>
> >>> I run a simulation of a hexamer and want to calculate RMSD values of
> >>> hairpins found in each monomer. For that I want to align the protein
> >>> body. When I aligned the first two frames in Chimera,
> >>
> >> You don't say what command you used to do the alignment in Chimera, or, for
> >> that matter, what commands you using in cpptraj. The latter would not place
> >> monomer 3 on top of monomer 1 unless you had some specific arguments that
> >> requested that.
> >
> > As Dave said, it would be best to post the actual input you tried, and
> > if you didn't get the result you expected something we (I) could use
> > to reproduce the issue (topology, coords, input, etc).
> >
> >> [Aside-- Dan, the description of the 'align' command in the manual is
> >> circular: it just says that the 'align' command "aligns the structure". What
> >> is the difference between this and 'rms'?]
> >
> > The 'align' command is just a bare-bones implementation of best-fit
> > 'rms' without creating a data set or any other functionality like
> > per-residue rms calc. etc. Guess I should be more clear in the manual
> > (boy if I had a nickel for every time I said that...).
> >
> > -Dan
> >
> >>
> >> .....dac
> >>
> >>
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Received on Wed Jun 16 2021 - 12:30:02 PDT
