Hello,
Adding "rms :1-237” after "image :238-244” will have the effect to rotated and translated each structure so as to minimize the RMSD to the reference.
Hope that helps.
Best regards,
Jean-Marc
> On 20 Jul 2016, at 22:15, Fabrício Bracht <fabracht1.gmail.com> wrote:
>
> Hi. I was wondering if there is a way to remove the rotation of a protein
> during cpptraj post-processing. I want to obtain an imaged trajectory with
> the closest water molecules to a specified residue, but so far, I have not
> been able to produce a trajectory without the rotation of the protein. The
> purpose is simply to improve visualization. Here is what I have come up to
> this far:
>
> trajin ../mdcrd.prod01
> trajin ../mdcrd.prod02
> trajin ../mdcrd.prod03
> reference restrt.min01
> center :1-237 reference
> image :238-244
> closest 10 :237 first closestout closestmols.dat outprefix strip
> trajout md_complete.mdcrd netcdf nobox
> go
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Received on Wed Jul 20 2016 - 13:30:04 PDT
