[gmx-users] residue SASA

[Diego Enry Gomes]

There's a quick & dirty workaround. You can write a script to "g_sas" each frame individually, writing many output files. Then grab the results from there.


Sent from my iPhone

On Jul 7, 2011, at 9:17 PM, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:

> 
> 
> ahmet yıldırım wrote:
>> There are hydrophilic and hydrophobic SASA values versus simulation time in the output file (area.xvg). I want to hydrophilic and hydrophobic SASA values versus residue.
> 
> That's not implemented, but it would probably be rather easy to modify the code to do so.
> 
> -Justin
> 
>> 2011/7/7 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>    ahmet yıldırım wrote:
>>        Dear users,
>>        I want to calculate hydrophilic and hyrophobic SASA value of
>>        each residue in protein. I used a command as the following:
>>        g_sas -f run.xtc -s run.tpr -or protein_protein.xvg
>>        Select a group for calculation of surface and a group for output
>>        select a group: 1 (protein)
>>        select a group: 2 (protein)
>>        But there is SASA value of each residue in the output file. How
>>        can I seperate the residues as a hydrophilic and hyrophobic SASA?
>>    This is already in the output file.  Check the legends of area.xvg
>>    and you will see.
>>    -Justin
>>    --     ==============================__==========
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>>    <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>    ==============================__==========
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>> -- 
>> Ahmet YILDIRIM
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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