I ran antigen-antibody MD simulation of 100ns by using gromacs. I follow "Lysozyme in Water" Bevan Lab tutorial to performed simulation. My PDB structure contain 3 chains, chain A (antibody-light chain), chain B (antibody heavy chain) and chain C (antigen). I calculate RMSD by using g_rms command it give rmsd of my all protein chains. But now I want to calculate antigen rmsd only. Is there any possible way to calculate RSMD of antigen?
You can save as a trajectory the coordinates of only the chain you are interested, for example using VMD program. The same you have to do for the reference structure. Then call g_rms for the new trajectory.
Hiqmet Kamberaj : How i can save my interested chain trajectories because my xtc file contains trajectories of all chains.
You can use the VMD program. First, open the complete trajectory (i.e., with all chains.) Then, do save coordinates, and chose the trajectory (gromacs option) with selection of the chain you are interested in the selection box. The same you can do it for the reference structure.
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