[gmx-users] Re: g_sas and vdwradii.dat

[Justin A. Lemkul]

Please disregard; I made a typo when selecting my index groups.

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
> 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
>
> ========================================
>
> 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/
>
> ========================================



========================================

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/

========================================