[gmx-users] Reg: RMSD calculation of a certain portion of protein

[Justin A. Lemkul]

Rohit Farmer wrote:
> Hi All,
> 
> Is there any way of calculating RMSD of only a certain portion of 
> protein structure after simulation. Like in Amber ptraj utility has this 
> option to mask out certain portion in RMSD.
> 

Yes, use an index group containing the residues/atoms of interest.

-Justin

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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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