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

[bharat gupta]

On Fri, Jan 21, 2011 at 3:32 AM, Justin A. Lemkul <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>
>>
>>
>>
>>
>>
>> --
>> 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
>
> ========================================
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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 ??


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
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