[gmx-users] g_sas

[Daniel Rigden]

Dear all

Sorry if this is a basic question, but I'm confused.  
I'd like to monitor the solvent-accessible surface area of two
particular residues in a large protein during the trajectory.  If I
provide an index file of one of those residues, then g_sas seems to
ignore the rest of the protein in calculating its surface area.  If, on
the other hand, I ask for surface area by residue or by atom, then I get
a list for one particular time point, not a set of measurements
throughout the trajectory.  How to monitor one residue in the context of
the whole protein?

Thanks

Daniel

-- 
Dr Daniel John Rigden                     Tel:(+44) 151 795 4467
School of Biological Sciences             FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool
Crown St.,
Liverpool L69 7ZB, U.K.