[gmx-users] residue SASA
Diego Enry Gomes
diego.enry at gmail.com
Thu Jul 7 23:06:31 CEST 2011
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.
>> 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 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
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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