[gmx-users] Re: g_rmsf

[bharat gupta]

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
>>
>>    ========================================
>>    --     gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at 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 the www
>>    interface or send it to gmx-users-request at gromacs.org
>>    <mailto:gmx-users-request at gromacs.org>.
>>
>>    Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at 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 the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110208/a25134ae/attachment.html>