You meant 'rmsd'? If yes, you can specify reference mask as you want. Check the manual for that.
An example: https://github.com/Amber-MD/cpptraj/blob/1a6ceaa7703c9d694c6b0717cf2c2c8f05353469/test/Test_General/RunTest.sh#L38-L39
Hai
> On Apr 8, 2017, at 2:31 PM, James Kress <jimkress_58.kressworks.org> wrote:
>
>
> I have two pdb files each containing a single piece of dsDNA. In file1.pdb
> the DNA has 24 residues. In file2.pdb the DNA has 28 residues.
>
> I wish to use residues 3-10, 15-22 in file1 as a reference for comparison
> with residues 4-11, 18-25 of file2. File2 is a 1ns trajectory of solvated
> dsDNA. File1 is a single frame of unsolvated dsDNA.
>
> How do I do this using cpptraj? I have the prmtop files for both File1 and
> File2.
>
> Any help would be appreciated.
>
> Jim Kress
>
>
>
>
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Received on Sun Apr 09 2017 - 02:00:02 PDT
