[gmx-users] Re: g_rmsf

[bharat gupta]

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 ..

Pls help ??

On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul <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>
>>
>>
> --
> ========================================
>
> 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
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