Re: [gmx-users] Re: g_rmsf

2011-02-08 Thread Mark Abraham 

On 9/02/2011 4:52 PM, bharat gupta wrote:

Tsjerk,

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 ?? ...


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.


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 ??


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.


I also want to know how can I calculate the distance between two beta 
strands (which are connected by a loop)


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.


Mark


...

On Tue, Feb 8, 2011 at 9:26 PM, Tsjerk Wassenaar > wrote:


We can't know that. We don't have your files (and we don't want them).
Check what you did, and what index groups you have. Write out the
structure for the index group and have a look. We're not a substitute
for your brain here... :p

Cheers,

Tsjerk

On Wed, Feb 9, 2011 at 6:20 AM, bharat gupta
mailto:bharat.85.m...@gmail.com>> wrote:
> 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 ??
>
> On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar
mailto:tsje...@gmail.com>> wrote:
>>
>> Hi Bharat,
>>
>> You can do it with post-processing the data you obtain from
g_rmfs, if
>> it's okay that the fit uses all residues in either case. Otherwise,
>> you can make an two index files, including only the residues
that are
>> common to both.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta
mailto:bharat.85.m...@gmail.com>>
>> wrote:
>> > 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
mailto:jalem...@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
mailto:jalem...@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 fi

Re: [gmx-users] Re: g_rmsf

2011-02-08 Thread bharat gupta 
Tsjerk,

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 ?? ...

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 ??

I also want to know how can I calculate the distance between two beta
strands (which are connected by a loop) ...

On Tue, Feb 8, 2011 at 9:26 PM, Tsjerk Wassenaar  wrote:

> We can't know that. We don't have your files (and we don't want them).
> Check what you did, and what index groups you have. Write out the
> structure for the index group and have a look. We're not a substitute
> for your brain here... :p
>
> Cheers,
>
> Tsjerk
>
> On Wed, Feb 9, 2011 at 6:20 AM, bharat gupta 
> wrote:
> > 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 ??
> >
> > On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar 
> wrote:
> >>
> >> Hi Bharat,
> >>
> >> You can do it with post-processing the data you obtain from g_rmfs, if
> >> it's okay that the fit uses all residues in either case. Otherwise,
> >> you can make an two index files, including only the residues that are
> >> common to both.
> >>
> >> Hope it helps,
> >>
> >> Tsjerk
> >>
> >> On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta 
> >> wrote:
> >> > 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 
> >> > 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  >> >>> > 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 : monu46...@yahoo.com 
> >> >>>>
> >> >>>
> >> >>>
> >> >>>-- 
> >> >>>
> >> >>>Justin A. Lemkul
> >> >>>Ph.D. Candidate
> >> >>>ICTAS Doctoral Scholar
> >> >>>MILES-IGERT Trainee
> >> >>>Department of Biochemistry
> >> >>>Virginia Tech
> >> >>>Blacksburg, VA
> >> >>>jalemk

Re: [gmx-users] Re: g_rmsf

2011-02-08 Thread Tsjerk Wassenaar 
We can't know that. We don't have your files (and we don't want them).
Check what you did, and what index groups you have. Write out the
structure for the index group and have a look. We're not a substitute
for your brain here... :p

Cheers,

Tsjerk

On Wed, Feb 9, 2011 at 6:20 AM, bharat gupta  wrote:
> 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 ??
>
> On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar  wrote:
>>
>> Hi Bharat,
>>
>> You can do it with post-processing the data you obtain from g_rmfs, if
>> it's okay that the fit uses all residues in either case. Otherwise,
>> you can make an two index files, including only the residues that are
>> common to both.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta 
>> wrote:
>> > 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 
>> > 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 > >>> > 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 : monu46...@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@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-requ...@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 : monu46...@yahoo.com 
>> >>>
>>

Re: [gmx-users] Re: g_rmsf

2011-02-08 Thread bharat gupta 
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 ??

On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar  wrote:

> Hi Bharat,
>
> You can do it with post-processing the data you obtain from g_rmfs, if
> it's okay that the fit uses all residues in either case. Otherwise,
> you can make an two index files, including only the residues that are
> common to both.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta 
> wrote:
> > 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 
> 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  >>> > 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 : monu46...@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 listgmx-users@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-requ...@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 : monu46...@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 listgmx-users@gromacs.org
> >> http://lists.gromacs.org/ma

Re: [gmx-users] Re: g_rmsf

2011-02-08 Thread bipin singh 
You calculate rmsf of both proteins separately and then plot them together
and look the region of your interest..

On Wed, Feb 9, 2011 at 10:28, bharat gupta  wrote:

> 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  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 >> jalem...@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 : monu46...@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 listgmx-users@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-requ...@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 : monu46...@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 listgmx-users@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-requ...@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 : monu

Re: [gmx-users] Re: g_rmsf

2011-02-08 Thread Tsjerk Wassenaar 
Hi Bharat,

You can do it with post-processing the data you obtain from g_rmfs, if
it's okay that the fit uses all residues in either case. Otherwise,
you can make an two index files, including only the residues that are
common to both.

Hope it helps,

Tsjerk

On Wed, Feb 9, 2011 at 5:58 AM, bharat gupta  wrote:
> 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  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 >> > 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 : monu46...@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@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-requ...@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 : monu46...@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@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-requ...@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
> Bu

Re: [gmx-users] Re: g_rmsf

2011-02-08 Thread 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  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 > jalem...@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 : monu46...@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 listgmx-users@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-requ...@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 : monu46...@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 listgmx-users@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-requ...@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 : monu46...@yahoo.com
-- 
gmx-users mailing listgmx-users@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 
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Re: [gmx-users] Re: g_rmsf

2011-02-08 Thread bipin singh 
try -res option

On Wed, Feb 9, 2011 at 08:51, Justin A. Lemkul  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 > jalem...@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 : monu46...@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 listgmx-users@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-requ...@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 : monu46...@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 listgmx-users@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-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
*
-
Thanks and regards
Bipin Singh
*
*
*
-- 
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Re: [gmx-users] Re: g_rmsf

2011-02-08 Thread Justin A. Lemkul 



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 > 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 : monu46...@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 listgmx-users@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-requ...@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 : monu46...@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 listgmx-users@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 
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Re: [gmx-users] Re: g_rmsf

2011-02-08 Thread 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  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 : monu46...@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 listgmx-users@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-requ...@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 : monu46...@yahoo.com
-- 
gmx-users mailing listgmx-users@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!
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: g_rmsf

2011-02-08 Thread Justin A. Lemkul 



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 : monu46...@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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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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[gmx-users] Re: g_rmsf

2011-02-08 Thread bharat gupta 
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 ??

-- 
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 : monu46...@yahoo.com
-- 
gmx-users mailing listgmx-users@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 
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