[gmx-users] Re: g_rmsf

[bipin singh]

try -res option

On Wed, Feb 9, 2011 at 08:51, 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
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>>        Mobile no. - 010-5818-3680
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>>        <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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-- 
*
---------------------------------
Thanks and regards
Bipin Singh
*
*
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