[gmx-users] G_sas change in hydrophilic and hydrophobic surface area
jalemkul at vt.edu
Thu Nov 22 19:02:21 CET 2012
On 11/22/12 2:36 AM, rama david wrote:
> Dear user ,
> I simulate the two protein in random coil position, when they come close
> they form antiparallel beta sheet structure.
> I want to calculate the change in hydrophilic and hydrophobic surface
> area over my simulation time.
> For usig g_sas Should I have to make the different index group for
> hydrophilic and hydrophobic residues
> Or should only have to select the option protein both the time.
The whole protein should always be the group for the surface calculation.
Whatever subset of those atoms (i.e. residues of interest) can be the output group.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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