Preparing a protein-only DCD file (removing waters)

Using catdcd

Use catdcd with the -i flag to prepare a protein-only DCD. The unix way to prepare the index file is

awk '{for (i=0 ; i < 434 ; i++) print i}'

where 434 is the number of atoms of the solute.

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Using carma

If your macromolecular component has segids, say, A and B, then you can in one step remove waters, translations and rotations with carma :

carma -v -fit -atmid "ALLID" -segid " A   " -segid " B   " my.dcd my.psf

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Preparation of a protein-only PSF

You will also need a protein-only PSF file. You can do this with an xplor script in the spirit of :

structure @ionized.psf end
delete selection=( resname TIP3 or resname SOD or resname CLA) end
write structure output=protein.psf end
stop

, or,

structure @ionized.psf end
delete selection=( not (segid="A   " or segid="B   ")) end
write structure output=protein.psf end
stop