[gmx-users] protein-ligand interaction

[ahmet yıldırım]

Dear Justin,

I used -res flag with the following command but I get pairs of values in the
output files. is there any mistake related with the command I used?
g_rmsf -s run.tpr -f run.xtc -o rmsf.xvg -od rmsdev.xvg -res



2011/5/29 <jalemkul at vt.edu>

> Quoting ahmet y?ld?r?m <ahmedo047 at gmail.com>:
>
>  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?
>>
>
> The -o output is RMSF; the -od output is RMSD.
>
>
>  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?
>>
>
> An index file should not be necessary.  By default, the output is per atom,
> so use the -res flag if you want the measurements averaged over all atoms in
> each residue.  The command is sufficient to measure the RMSD per residue.
>  Whether or not that is sufficient is up to you.
>
>  3. Furthermore, can you suggest the other analysis tools to see the effect
>> of the ligand *on protein*?
>>
>>
> You should identify the quantities you wish to measure, then read in the
> Gromacs manual about the different utility programs available.  You'll learn
> far more that way.
>
> -Justin
>
>
>  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
>>
>>
>
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
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> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>



-- 
Ahmet YILDIRIM
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