Removing global rotations-translations from a protein-only DCD file

Assuming that you have the solute-only DCD and PSF files, and that their names are native.dcd and native.psf, you can say

carma -v -fit -atmid "ALLID" native.psf native.dcd

This will produce two files : the file carma.fit-rms.dat contains a list of rms deviations from the starting structure (for all atoms) and can be plotted with something in the spirit of xmgr carma.fit-rms.dat. The second file is named carma.fitted.dcd and contains the new DCD file (with global translations and rotations removed). The new DCD file should work just fine with your existing native.psf. Don't forget to rename the carma.fitted.dcd file (to, say, fitted_all.dcd).

While you are at it, you can also prepare a CA-only (or, for DNA, P-only) DCD with rotations and translations removed :

carma -v -fit native.psf native.dcd

To view the resulting DCD file you need a CA-only (or P-only) PSF file. This you can prepare with xplor :

structure @native.psf end
delete selection=( not name ca ) end
write structure output=CA.psf end
stop