[gmx-users] Fwd: RMSD calculation of a specific region

[Justin A. Lemkul]

bharat gupta wrote:
> 
> 
> On Fri, Jan 21, 2011 at 3:32 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     bharat gupta wrote:
> 
> 
> 
>         I want to calculate the rmsd of amino acid 65 to 67 of two
>         simulated proteins with  loop replacement in another one to find
>         out how the position of these 3  amino acids change due to the
>         replacement of a loop region in same protein ... How can I
>         achieve it with gromacs...
> 
> 
>     Use g_rms with a suitable index group.
> 
>     -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>>
> 
> 
> 
> 
> 
>         -- 
>         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
> 
>     ========================================
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> 
> 
> I am not able to search some relevant document about creating index 
> group fro g_rms ... I found one i gromacs website 
> http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive but 
> this link doesnot explain much about it ... can u pls guide me to some 
> relevant link ??
>  

See the manual, section 8.1 and appendix D.83.  If you search the Gromacs site 
for "index group" you will find (among others):

http://www.gromacs.org/Documentation/File_Formats/Index_File

-Justin

>  
> I am stating my question here again :  I want to calculate the rmsd of 
> amino acid 65 to 67 of two simulated proteins with  loop replacement in 
> another one to find out how the position of these 3  amino acids change 
> due to the replacement of a loop region in same protein ... How can I 
> achieve it with gromacs...
>  
> 
> -- 
> 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

========================================