[gmx-users] G_sas change in hydrophilic and hydrophobic surface area
jalemkul at vt.edu
Thu Nov 22 20:15:05 CET 2012
On 11/22/12 1:54 PM, rama david wrote:
> Hi justin,
> Thank you for reply.
> As per your suggestion,
> 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.
> So as per your suggestion I have to select the protein as my option 1 and
> for output I have to select the hydrophilic residues or hydrophobic
> residues as per my choice ....Is these is right ??? or Am I wrong???
> ( That means I have to make to index file that contain two groups
> hydrophilic and hydrophobic residues.)
> Would you please tell me why not select the protein as output, as I am
> calculating the change in the hydrophilic and hydrophobic surface area of
You can certainly do that. Perhaps I misunderstood the original post. I
thought you were curious about the solvent exposure of certain residues. If you
only care about the evolution of total polar and nonpolar surface areas, then
choose Protein for both groups.
> As per the manual,
> The program will ask for a group for the surface calculation and a
> group for the output. The
> calculation group should always consists of all the non-solvent atoms in the
> system. The output group can be the whole or part of the calculation group.
> As two protein comes closer in simulation they formed the antiparrallel
> beta strand, I want to find the change in hydrophilic and hydrophobic
> surface area of protein...
> With Best Wishes and Regards,
> Rama david
> On Thu, Nov 22, 2012 at 11:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 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.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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