Create two index groups. One with 28-197 residues and second group with
2-27.

Supply this index file to gmx rms (if using 5.1) with -n option and select
28-197 as fit group and 2-27 for RMSD analysis.

Regards,

Sarath

On 20 September 2016 at 12:05, Seera Suryanarayana <paluso...@gmail.com>
wrote:

> Dear gromcas users,
>
> I have done simulations for 100ns for protein of my interest. The protein
> length is 197 residues and I fixed the positions one n-terminal residue and
> from 28th residue to 197 residues also fixed. My interest of area in
> protein is from 2 to 27 residues. Although I have done simulations for
> complete length of protein. I just want calculate the RMSD values for
> region between 2 to 27. If I use reference structure md_0_1.tpr, it gives
> RMSD for entire protein. But how to find RMSD for my interest of region (2
> - 27 residues)?   Kindly guide me how to do it.
>
> Thanks in advance
> Surya
> Graduate student
> India.
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