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2024-05-07
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2024-05-06
Editing revision 11 of Preparing a protein-only DCD file (removing waters)
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== Using catdcd == Use /catdcd/ with the <b>-i</b> flag to prepare a protein-only DCD. The unix way to prepare the index file is <code> awk '{for (i=0 ; i < 434 ; i++) print i}' </code> where <b>434</b> is the number of atoms of the solute. ------ == 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/ : <code> carma -v -fit -atmid "ALLID" -segid " A " -segid " B " my.dcd my.psf </code> ------ == 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 : <code> structure @ionized.psf end delete selection=( resname TIP3 or resname SOD or resname CLA) end write structure output=protein.psf end stop </code> , or, <code> structure @ionized.psf end delete selection=( not (segid="A " or segid="B ")) end write structure output=protein.psf end stop </code>
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