Dear users,
I am getting pairs of values in the output files as I said before. What is
this mean? Furthermore, though my system have 451 residue, it seems as 230
residue ( and 1th residue does not seem in the out files). What could be the
problem?
*
output file:*
# This file was created Sun May 29 22:33:05 2011
# by the following command:
# g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res
#
# g_rmsf is part of G R O M A C S:
#
# GROwing Monsters And Cloning Shrimps
#
@ title "RMS fluctuation"
@ xaxis label "Residue"
@ yaxis label "(nm)"
@TYPE xy
2 0.1217
3 0.0952
4 0.0760
5 0.0740
6 0.0613
7 0.0565
.............
227 0.0785
228 0.0955
229 0.1254
230 0.1352
2 0.1181
3 0.0851
4 0.0713
5 0.0674
6 0.0645
7 0.0631
8 0.0707
9 0.0699
........
228 0.1034
229 0.1161
230 0.1206
29 Mayıs 2011 19:28 tarihinde ahmet yıldırım <ahmedo...@gmail.com> yazdı:
> 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 <jalem...@vt.edu>
>
> Quoting ahmet y?ld?r?m <ahmedo...@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 <jalem...@vt.edu>
>>>
>>> Quoting ahmet y?ld?r?m <ahmedo...@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
>>>>
>>>> ========================================
>>>> --
>>>> gmx-users mailing list gmx-users@gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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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@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use thewww interface
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Ahmet YILDIRIM
>
--
Ahmet YILDIRIM
--
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