Thanks for the advice and while creating the index file for first 100 common residues it found that both structures shows different no.of atoms. .. how is that possible ??<br><br><div class="gmail_quote">On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Bharat,<br>
<br>
You can do it with post-processing the data you obtain from g_rmfs, if<br>
it's okay that the fit uses all residues in either case. Otherwise,<br>
you can make an two index files, including only the residues that are<br>
common to both.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta <<a href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>> wrote:<br>
> I used the -res option ... and I got the rmsf in terms of residues but still<br>
> the problem is that the two structures contain different amount of residues<br>
> due to loop replacement in one structure.. In that case how shall proceed to<br>
> check the effect of loop insertion on the overall topology of the protein..<br>
> pls guide ??<br>
><br>
> On Tue, Feb 8, 2011 at 7:21 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
>><br>
>><br>
>> bharat gupta wrote:<br>
>>><br>
>>> Actually after loop incorporation I want to check which region of the<br>
>>> protein shows much deviation , which I think can be done by plotting rmsf<br>
>>> values from both proteins.. but the problem here is that one structure which<br>
>>> contains loops has more no. of atoms as compared to other str. without loop<br>
>>> insertion .. so which way it can be analyzed ??<br>
>>><br>
>>> Also g_rmsf gives RMSF values for atoms of residues but not of residues<br>
>>> how can I get the values for residues ..<br>
>><br>
>> Please read g_rmsf -h.<br>
>><br>
>> -Justin<br>
>><br>
>>> Pls help ??<br>
>>><br>
>>> On Tue, Feb 8, 2011 at 6:57 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
>>> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>> wrote:<br>
>>><br>
>>><br>
>>><br>
>>> bharat gupta wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> I want to calculate the RMSF of residues and not of protein ...<br>
>>> how can this be done with g_rmsf..<br>
>>><br>
>>> Also I want to see the rmsf of certain residues .. for which I<br>
>>> created the .ndx file containint those residues only .. and<br>
>>> after using g_rmsf with index file gives the RMSF for whole<br>
>>> protein backbone and not for that index file residues ... what<br>
>>> shall I do to have RMSF of index file residues ??<br>
>>><br>
>>><br>
>>> The default output of g_rmsf is a plot of RMSF (of each residue) vs.<br>
>>> residue. No index file is required to obtain this, unless you want<br>
>>> to do the fitting to some custom group. Is this not what you want?<br>
>>><br>
>>> -Justin<br>
>>><br>
>>> -- Bharat<br>
>>> Ph.D. Candidate<br>
>>> Room No. : 7202A, 2nd Floor<br>
>>> Biomolecular Engineering Laboratory<br>
>>> Division of Chemical Engineering and Polymer Science<br>
>>> Pusan National University<br>
>>> Busan -609735<br>
>>> South Korea<br>
>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343<br>
>>> Mobile no. - 010-5818-3680<br>
>>> E-mail : <a href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a> <mailto:<a href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a>><br>
>>> <mailto:<a href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a> <mailto:<a href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a>>><br>
>>><br>
>>><br>
>>> -- ========================================<br>
>>><br>
>>> Justin A. Lemkul<br>
>>> Ph.D. Candidate<br>
>>> ICTAS Doctoral Scholar<br>
>>> MILES-IGERT Trainee<br>
>>> Department of Biochemistry<br>
>>> Virginia Tech<br>
>>> Blacksburg, VA<br>
>>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
>>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>>><br>
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>>><br>
>>> --<br>
>>> Bharat<br>
>>> Ph.D. Candidate<br>
>>> Room No. : 7202A, 2nd Floor<br>
>>> Biomolecular Engineering Laboratory<br>
>>> Division of Chemical Engineering and Polymer Science<br>
>>> Pusan National University<br>
>>> Busan -609735<br>
>>> South Korea<br>
>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343<br>
>>> Mobile no. - 010-5818-3680<br>
>>> E-mail : <a href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a> <mailto:<a href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a>><br>
>>><br>
>><br>
>> --<br>
>> ========================================<br>
>><br>
>> Justin A. Lemkul<br>
>> Ph.D. Candidate<br>
>> ICTAS Doctoral Scholar<br>
>> MILES-IGERT Trainee<br>
>> Department of Biochemistry<br>
>> Virginia Tech<br>
>> Blacksburg, VA<br>
>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>><br>
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><br>
><br>
> --<br>
> Bharat<br>
> Ph.D. Candidate<br>
> Room No. : 7202A, 2nd Floor<br>
> Biomolecular Engineering Laboratory<br>
> Division of Chemical Engineering and Polymer Science<br>
> Pusan National University<br>
> Busan -609735<br>
> South Korea<br>
> Lab phone no. - +82-51-510-3680, +82-51-583-8343<br>
> Mobile no. - 010-5818-3680<br>
> E-mail : <a href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a><br>
><br>
</div></div>> --<br>
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><br>
<br>
<br>
<br>
--<br>
</div>Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<div><div></div><div class="h5">--<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>