<div>you said you have used online server for superimposition ...<br></div><div>which one you used...</div><div>try TOPMATCH server....</div><br><div class="gmail_quote">On Sun, May 9, 2010 at 5:31 PM, Anupam Nath Jha <span dir="ltr"><<a href="mailto:anupam@mbu.iisc.ernet.in">anupam@mbu.iisc.ernet.in</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
Ok.<br>
<br>
But when I run this command<br>
<div class="im">g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out<br>
<br>
</div>it ask me groups... and that i thought is for fitting///<br>
<br>
for example -<br>
<br>
------------------------<br>
Select group for least squares fit<br>
Group 0 (C-alpha_chain1) has 249 elements<br>
Group 1 (C-alpha_chain2) has 249 elements<br>
Group 2 (C-alpha_chain3) has 249 elements<br>
Group 3 (C-alpha_chain4) has 249 elements<br>
Select a group: 0<br>
Selected 0: 'C-alpha_chain1'<br>
Select group for RMSD calculation<br>
Group 0 (C-alpha_chain1) has 249 elements<br>
Group 1 (C-alpha_chain2) has 249 elements<br>
Group 2 (C-alpha_chain3) has 249 elements<br>
Group 3 (C-alpha_chain4) has 249 elements<br>
Select a group:1<br>
Selected 1: 'C-alpha_chain2'<br>
<br>
---------------------------------<br>
<br>
Is it not superimposing these two chins and calculating RMSD between them???<br>
<br>
--<br>
<font color="#888888">anupam<br>
</font><div><div class="h5"><br>
<br>
> On 9/05/2010 9:29 PM, Justin A. Lemkul wrote:<br>
>><br>
>><br>
>> Anupam Nath Jha wrote:<br>
>>>><br>
>>>> Anupam Nath Jha wrote:<br>
>>>>> Dear all<br>
>>>>><br>
>>>>> I made an index file with 4 different groups for 4 different chains<br>
>>>>> (since my<br>
>>>>> protein is a tetramer) and then run<br>
>>>>><br>
>>>>> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out<br>
>>>>><br>
>>>>> to get the rmsd between two different monomers from the same structure,<br>
>>>>> it asked me two different groups and I gave 0 and 1.<br>
>>>>><br>
>>>>> The output file is like this<br>
>>>>><br>
>>>>> # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New<br>
>>>>> #<br>
>>>>> # g_rms is part of G R O M A C S:<br>
>>>>> #<br>
>>>>> # Grunge ROck MAChoS<br>
>>>>> #<br>
>>>>> @ title "RMSD"<br>
>>>>> @ xaxis label "Time (ps)"<br>
>>>>> @ yaxis label "RMSD (nm)"<br>
>>>>> @TYPE xy<br>
>>>>> @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1"<br>
>>>>> 0.0000000 0.0000001<br>
>>>>><br>
>>>> In the command you've given (with the same file for -s and -f),<br>
>>>> you're computing<br>
>>>> the RMSD at time zero, after fitting to the structure at time zero,<br>
>>>> so the RMSD<br>
>>>> must be zero.<br>
>>><br>
>>><br>
>>> but I am giving different groups (as chains). I am trying to get RMSD<br>
>>> between<br>
>>> two monomers in same structure so what's wrong in that....<br>
>>><br>
>><br>
>> It doesn't matter. The structure for calculation (-f) and the reference<br>
>> structure (-s) are identical, so the RMSD has to be zero, regardless of<br>
>> the fitting group and calculation groups chosen.<br>
><br>
> Exactly. Only if you can fit group A from one file to group B from a<br>
> file (which may or may not be the same file) can Anupam do this<br>
> calculation. g_rms seems not to allow this.<br>
><br>
> Instead, Anupam should use trjconv or editconf to select groups<br>
> beforehand, as I think I suggested a few days back. Thus (say) editconf<br>
> produces file_with_group_A.pdb and editconf produces<br>
> file_with_group_B.pdb, which allows g_rms -f file_with_group_A -s<br>
> file_with_group_B. This will work if the two groups have the same atoms<br>
> in matching orders, which should be the case for a tetramer setup.<br>
><br>
> Mark<br>
><br>
>>>>> so the rmsd = 0.0000001<br>
>>>>><br>
>>>>> whereas when I use online server it gives me 1.4.<br>
>>>>><br>
>>>>> so what am I doing wrong?<br>
>>>>><br>
>>>> Then whatever you're giving the online server is different. The Gromacs<br>
>>>> calculation seems to be correct.<br>
>>>><br>
>>>> -Justin<br>
>>>><br>
>>><br>
>>><br>
>>><br>
>>>>> regrads<br>
>>>>> anupam<br>
>>>>><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>
>>>> ========================================<br>
>>>> --<br>
>>>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>>>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
>>>> posting!<br>
>>>> Please don't post (un)subscribe requests to the list. Use the<br>
>>>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>>>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
>>>><br>
>>>> --<br>
>>>> This message has been scanned for viruses and<br>
>>>> dangerous content by MailScanner, and is<br>
>>>> believed to be clean.<br>
>>>><br>
>>>><br>
>>><br>
>>><br>
>><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
> --<br>
> This message has been scanned for viruses and<br>
> dangerous content by MailScanner, and is<br>
> believed to be clean.<br>
><br>
><br>
<br>
<br>
--<br>
</div></div><div class="im">Science is facts; just as houses are made of stone, so is science is made of<br>
facts; but a pile of stones is not a house, and a collection of facts is not<br>
necessarily science.<br>
<br>
Anupam Nath Jha<br>
Ph. D. Student<br>
Saraswathi Vishveshwara Lab<br>
Molecular Biophysics Unit<br>
IISc,Bangalore-560012<br>
Karnataka<br>
Ph. no.-22932611<br>
<br>
<br>
<br>
--<br>
</div><div><div class="h5">This message has been scanned for viruses and<br>
dangerous content by MailScanner, and is<br>
believed to be clean.<br>
<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharath.K.Chakravarthi<br>Ph:9535629260<br>