[gmx-users] g_sas and vdwradii.dat

Paul Whitford pwhitfor at ctbp.ucsd.edu
Thu Jun 5 00:20:43 CEST 2008

Gromacs users,

I have 3 easy questions regarding the use of g_sas

1)  I am trying to understand exactly how gromacs computed the SAS.  I
looked at vdwradii.dat and it says

; Very approximate VanderWaals radii
; only used for drawing atoms as balls or for calculating atomic overlap.

Does atomic overlap include SAS calculations?  If not, where does g_sas get
the sphere sizes when making the calculation?

2) How can I tell gromacs to look at a different file for atom sizes?  I
would like to compare the SAS for a C-alpha model with varying sizes for the
CA beads.

3) How goes g_sas determine which atoms are hydrophobic and hydrophilic?  I
would like to call some CA atoms hydrophobic and others hydrophilic.

Thanks in advance!

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