On Tue, Aug 30, 2011 at 10:41 AM, Jan-Philip Gehrcke <
jgehrcke.googlemail.com> wrote:
> Hey.
>
> Using cpptraj, I am interested in how to get the RMSD of a certain
> region within two structures after fitting these structures using
> another region. The same question was already answered for ptraj:
> http://archive.ambermd.org/201102/0128.html
>
> Quote by Dan:
> "
> reference refstruct.rst7
> rms reference :1-100
> rms reference :50-55 nofit out rmsd.dat
>
> The first rms command performs the best fit, then the second rms
> command calculates the rmsd you want without changing the fit from the
> first rms command.
> "
>
> This is what I propose for cpptraj (for my system):
>
> parm topology.top
> trajin traj1.mdcrd
> rmsd :1-150 first
>
This aligns all structures by minimizing the RMS of that structure against
the first structure using only residues 1-150 when calculating the RMS.
> rmsd :151-161 first nofit out rmsd.dat
>
This calculates the RMS between each structure using residues 151-161
*without* first doing a fit to that region. Thus, the structures will still
be aligned according to the RMS command above (since that one is executed
first).
> Would that for each frame
> 1) align the residues 1-150 of the current frame to the residues 1-150
> of the first frame and then
> 2) calculate the RMSD for residues 151 to 161 with the alignment from
> (1) (again current frame vs. first frame)?
>
Yes.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Aug 30 2011 - 08:30:02 PDT
