[gmx-users] protein-ligand interaction

[ahmet yıldırım]

Dear Justin,

You said "  You can get a per-residue RMSD by using g_rmsf -od to see the
effect of the ligand on each residue."
1. Can you explain the difference between what goes into the -o file, and
what goes into the -od file?
2. How should I create a index file to see the effect of the ligand on each
residue? Do I have to create the index file?
g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg
Is this command sufficient to see the effect of the ligand on each residue?
3. Furthermore, can you suggest the other analysis tools to see the effect
of the ligand *on protein*?

Thanks in advance

2011/5/28 <jalemkul at vt.edu>

> Quoting ahmet y?ld?r?m <ahmedo047 at gmail.com>:
>
>  Dear users,
>>
>> I want to investigate *Ligand effect *on the protein .
>> To investigation the interaction of protein-ligand:
>> *RMSD calculations:*
>> 1.
>> a) RMSD of Backbone
>> b) RMSD of Backbone+ligand
>> 2.
>> a) RMSD of Protein
>> b) RMSD of Protein+ligand
>> 3.
>> a) RMSD of Protein-H
>> b) RMSD of Protein-H+ligand
>> Which one would you recommend ( 1., 2., and 2.choice)?
>>
>>
> Unless the effect of your ligand is very large (i.e., the whole protein is
> significantly more or less stable in the presence of the ligand), then
> likely none of these analyses will be particularly illustrative as they are
> not very sensitive to small changes.  You can get a per-residue RMSD by
> using g_rmsf -od to see the effect of the ligand on each residue.
>  Otherwise, the most common quantity measured is backbone RMSD.
>
> -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
>
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-- 
Ahmet YILDIRIM
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