[gmx-users] Re: g_rmsf

[bipin singh]

You calculate rmsf of both proteins separately and then plot them together
and look the region of your interest......

On Wed, Feb 9, 2011 at 10:28, 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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-- 
*
---------------------------------
Thanks and regards
Bipin Singh
*
*
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