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On 9/02/2011 4:52 PM, bharat gupta wrote:
<blockquote
cite="mid:AANLkTimySHNK2Zy8csPK3tGukdkKYsadTst1NDrmAt2Q@mail.gmail.com"
type="cite">
<div>Tsjerk,</div>
<div><br>
</div>
Sorry for asking that .. actually I made a silly mistake while
selecting residues.. After plotting the graphs for common regions
I found that first 100 amino acids shows a lot of fluctuations
(compared to the one without any loop insertion) ... Does the
insertion caused a great change in the over topology ... what
could be the answer for this ?? ... <br>
</blockquote>
<br>
Maybe the insertion does cause a change. Isn't that one of the
things you're trying to see? Maybe you've not got enough data. Maybe
you've not made a single-variable change. You have to have done a
pair of simulations (whose difference is known, well-defined and
relevant) for long enough time for the observables to converge
within a simulation in order to do a meaningful comparison of those
observables across those simulations.<br>
<br>
<blockquote
cite="mid:AANLkTimySHNK2Zy8csPK3tGukdkKYsadTst1NDrmAt2Q@mail.gmail.com"
type="cite">
<div>Is there any other way to check the effect loop insertion on
the topology of protein ... I heard of essential dynamics method
and I asked u earlier about the same .. u told me that 3ns time
is small for such analysis but I have found a paper (published
in 1999) that has done ED analysis on a 1ns simulated trajectory
.. Whether doing such analysis for my data will be acceptable ??</div>
</blockquote>
<br>
Computer power doubles about every 18 months. Things that were
too-short-but-acceptable a decade ago often will no longer be
acceptable. In the 80s people did vacuum MD with 0.7nm cutoffs,
which would be laughed at now.<br>
<br>
<blockquote
cite="mid:AANLkTimySHNK2Zy8csPK3tGukdkKYsadTst1NDrmAt2Q@mail.gmail.com"
type="cite">
<div>I also want to know how can I calculate the distance between
two beta strands (which are connected by a loop) </div>
</blockquote>
<br>
Have a look at the short descriptions of the the tools in manual
section 7.4 or 8, and then look up the detailed descriptions of
useful-sounding tools in the appendix.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTimySHNK2Zy8csPK3tGukdkKYsadTst1NDrmAt2Q@mail.gmail.com"
type="cite">
<div>...<br>
<br>
<div class="gmail_quote">On Tue, Feb 8, 2011 at 9:26 PM, Tsjerk
Wassenaar <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">We can't know that. We don't have your
files (and we don't want them).<br>
Check what you did, and what index groups you have. Write
out the<br>
structure for the index group and have a look. We're not a
substitute<br>
for your brain here... :p<br>
<br>
Cheers,<br>
<font color="#888888"><br>
Tsjerk<br>
</font>
<div>
<div class="h5"><br>
On Wed, Feb 9, 2011 at 6:20 AM, bharat gupta <<a
moz-do-not-send="true"
href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>>
wrote:<br>
> Thanks for the advice and while creating the index
file for first 100 common<br>
> residues it found that both structures shows
different no.of atoms. .. how<br>
> is that possible ??<br>
><br>
> On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar
<<a moz-do-not-send="true"
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>>
wrote:<br>
>><br>
>> 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>
>><br>
>> On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta
<<a moz-do-not-send="true"
href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>><br>
>> wrote:<br>
>> > I used the -res option ... and I got the
rmsf in terms of residues but<br>
>> > still<br>
>> > the problem is that the two structures
contain different amount of<br>
>> > residues<br>
>> > due to loop replacement in one structure..
In that case how shall<br>
>> > proceed to<br>
>> > check the effect of loop insertion on the
overall topology of the<br>
>> > protein..<br>
>> > pls guide ??<br>
>> ><br>
>> > On Tue, Feb 8, 2011 at 7:21 PM, Justin A.
Lemkul <<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
>> > 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<br>
>> >>> rmsf<br>
>> >>> values from both proteins.. but
the problem here is that one structure<br>
>> >>> which<br>
>> >>> contains loops has more no. of
atoms as compared to other str. without<br>
>> >>> 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<br>
>> >>> 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 moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
>> >>> <mailto:<a
moz-do-not-send="true" 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)<br>
>> >>> 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
moz-do-not-send="true"
href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a>
<mailto:<a moz-do-not-send="true"
href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a>><br>
>> >>> <mailto:<a
moz-do-not-send="true"
href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a>
<mailto:<a moz-do-not-send="true"
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
moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> <<a
moz-do-not-send="true" href="http://vt.edu"
target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
>> >>> <a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>> >>><br>
>> >>>
========================================<br>
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>> >>><br>
>> >>><br>
>> >>><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
moz-do-not-send="true"
href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a>
<mailto:<a moz-do-not-send="true"
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 moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a> |
(540) 231-9080<br>
>> >> <a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>> >><br>
>> >>
========================================<br>
>> >> --<br>
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>> ><br>
>> ><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 moz-do-not-send="true"
href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a><br>
>> ><br>
>> > --<br>
>> > gmx-users mailing list <a
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>> ><br>
>><br>
>><br>
>><br>
>> --<br>
>> 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>
>> --<br>
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><br>
><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 moz-do-not-send="true"
href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a><br>
><br>
> --<br>
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><br>
<br>
<br>
<br>
--<br>
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>
--<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 moz-do-not-send="true"
href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div>
<br>
</div>
</blockquote>
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