VMD-L Mailing List

From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Sun Jul 20 2008 - 16:28:04 CDT

Hello,
I am trying to generate some rdfs for systems that I have already run. I
want to do these using the protein surface as one selection. I know that
using the selection "Protein and Surface" only implies "Not Buried" which
removes hydrophobic residues from the selection set, but I want to see the
actual atoms, including any hydrophobic ones that have at least some SASA,
while also not including polar atoms that are actually buried, e.g. at the
dimer interface. I know it may not be exactly correct since I should have
to determine the SASA for each frame, but to make this doable in a
reasonable amount of time and since my protein has an average RMSD of ~1.2A
the atoms that make up the set from frame 0 should not deviate that much, I
assume.

So does anyone know how to define a selection of SASA > 0 atoms for use in
gofr?

Thanks

Chris