[gmx-users] Protein-ligand simulation

[Ankita naithani]

Hi,

I recently ran a simulation with the complete structure of my protein
alongwith the ligands. I was running some analysis and was trying out
the Principal component analysis.
I used the g_covar tool to get the eigenvalues and eigenvectors for
protein back bone. However, when I try to use g_covar for the whole
system, it shows me segmentation fault. My problem is that I want to
see the simulation of my protein and ligand together as a whole. I ran
g_covar individually for all the ligands and saw the first eigenvector
movie in pymol and similarly for protein backbone. But I would really
like to see the ligand and protein dynamics together because when I
see the eigenvector individually, the ligand is moving in a direction
probably towards the binding site and it would be quite helpful if
anyone could suggest how can I possibly view them together.




-- 
Ankita Naithani