VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Nov 24 2007 - 10:50:32 CST

Once I have aligned a protein over a membrane, is any command to get rid of
lipid and water residues that overlap the protein, plus a margin of say 1.5A?
Better if the command is per residue, rather that per all overlapping atoms or
residues.

Also, is it any command to list overlapping residues? I want to check for any
possible steric clashes.

Why am I not using the plugin combine? I was unable to get it working with my
systems. However, once the cavity is created in the membrane, and I have the
coordinates of the protein now fitting the cavity, I have the means to combine
both, getting a usable pdb file.

Thanks for your understanding toward a guy with only one foot in VMD.

francesco pietra

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