[gmx-users] the effect of the ligand on each residue

[ahmet yıldırım]

Dear Justin,

Thanks for your reply. Well, to explore the effect of the ligand on protein

g_mindist -f run.xtc -s run.tpr -od mindist.xvg -on numcont.xvg
Select a group: 1
Selected 1: 'Protein'
Select a group: 13
Selected 13: 'LİGAND'

Does this choice make sense?


30 Haziran 2011 14:43 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> I want to see the effect of the ligand on each residue using the following
>> command:
>> g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res
>>
>> Select group(s) for root mean square calculation
>> Select a group: ?
>> Which group should I choose?
>>
>>
> The group that is most meaningful to you, based on the behavior observed in
> the trajectory.  You can analyze backbone, sidechain, or all protein atoms
> separately.  Several iterations may be informative, using several different
> groups.
>
> -Justin
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Ahmet YILDIRIM
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