[gmx-users] g_sas and vdwradii.dat
pwhitfor at ctbp.ucsd.edu
Thu Jun 5 00:20:43 CEST 2008
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
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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