[gmx-users] g_sas and vdwradii.dat

[Justin A. Lemkul]

Hi all,

I recently completed several simulations of pure DPPC bilayers (128 lipids, 64
per leaflet, from Tieleman's site), and am processing the output.  Of interest
to me is the SASA, so I'm using g_sas.  I ran the command:

g_sas -f md_0_100.xtc -s md.tpr -n sas.ndx

(selecting solvent for the calculation, and a subset of my lipids for output)

I get the following message:

0 out of 3200 atoms were classified as hydrophobic

But yet, if I let the calculation go anyway, I get seemingly reasonable values
for hydrophobic, hydrophilic, and total SASA.  It is odd to me that in a
membrane, none of the atoms are considered hydrophobic.

Should I be concerned about my results being incorrect, or is it simply because
the atom types of the acyl chains are unrecognized as standard by g_sas?  I
have learned not to ignore such strange messages :-)

Thanks in advance.

-Justin

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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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