[gmx-users] Re: g_rmsf

[Tsjerk Wassenaar]

Hi Bharat,

You can do it with post-processing the data you obtain from g_rmfs, if
it's okay that the fit uses all residues in either case. Otherwise,
you can make an two index files, including only the residues that are
common to both.

Hope it helps,

Tsjerk

On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta <bharat.85.monu at gmail.com> wrote:
> I used the -res option ... and I got the rmsf in terms of residues but still
> the problem is that the two structures contain different amount of residues
> due to loop replacement in one structure.. In that case how shall proceed to
> check the effect of loop insertion on the overall topology of the protein..
> pls guide ??
>
> On Tue, Feb 8, 2011 at 7:21 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> bharat gupta wrote:
>>>
>>> Actually after loop incorporation I want to check which region of the
>>> protein shows much deviation , which I think can be done by plotting rmsf
>>> values from both proteins.. but the problem here is that one structure which
>>> contains loops has more no. of atoms as compared to other str. without loop
>>> insertion .. so which way it can be analyzed ??
>>>
>>> Also g_rmsf gives RMSF values for atoms of residues but not of residues
>>> how can I get the values for residues ..
>>
>> Please read g_rmsf -h.
>>
>> -Justin
>>
>>> Pls help ??
>>>
>>> On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul <jalemkul at vt.edu
>>> <mailto:jalemkul at vt.edu>> wrote:
>>>
>>>
>>>
>>>    bharat gupta wrote:
>>>
>>>        Hi,
>>>
>>>        I want to calculate the RMSF of residues and not of protein ...
>>>        how can this be done with g_rmsf..
>>>
>>>        Also I want to see the rmsf of certain residues .. for which I
>>>        created the .ndx file containint those residues only .. and
>>>        after using g_rmsf with index file gives the RMSF for whole
>>>        protein backbone and not for that index file residues ... what
>>>        shall I do to have RMSF of index file residues ??
>>>
>>>
>>>    The default output of g_rmsf is a plot of RMSF (of each residue) vs.
>>>    residue. No index file is required to obtain this, unless you want
>>>    to do the fitting to some custom group.  Is this not what you want?
>>>
>>>    -Justin
>>>
>>>        --         Bharat
>>>        Ph.D. Candidate
>>>        Room No. : 7202A, 2nd Floor
>>>        Biomolecular Engineering Laboratory
>>>        Division of Chemical Engineering and Polymer Science
>>>        Pusan National University
>>>        Busan -609735
>>>        South Korea
>>>        Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>>        Mobile no. - 010-5818-3680
>>>        E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>>>        <mailto:monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>>
>>>
>>>
>>>    --     ========================================
>>>
>>>    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
>>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>    ========================================
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>>>
>>>
>>> --
>>> Bharat
>>> Ph.D. Candidate
>>> Room No. : 7202A, 2nd Floor
>>> Biomolecular Engineering Laboratory
>>> Division of Chemical Engineering and Polymer Science
>>> Pusan National University
>>> Busan -609735
>>> South Korea
>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>> Mobile no. - 010-5818-3680
>>> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>>>
>>
>> --
>> ========================================
>>
>> 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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>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands