MBG wiki: Editing 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

<code>
carma -v -fit -atmid "ALLID" native.psf native.dcd
</code>

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, <b>fitted_all.dcd</b>).

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

<code>
carma -v -fit native.psf native.dcd
</code>

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

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

Summary:

This change is a minor edit.

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