I have read a couple of tutorials and am trying to incorporate the basic analysis tools available in gromacs like g_rmsd, g_rmsf, g_rms, g_covar, etc. But as I have recently started, I am confused about how to proceed in an appropriate direction. I am interested in studying the allosteric movements in my protein. Any help for me to channelize properly would be really kind.
Hi Stephane,
Yes indeed my system has ligands. For the stability, fluctuation with or without ligand, should I be running another simulation after removing my ligands? I have done rmsf, rmsd, g_hbonds and g_saltbr plots. Also, I used g_covar, I exactly don't know how to begin using g_covar best to look into protein domain motions, could you please guide me further on this?
You can use Principal component analysis and/or Covariance nets. I suggest that you read the paper of Elena Papaleo of her program Xpyder (and related papers). The paper "Thrombin allosteric modulation revisited: a molecular dynamics study" of Hermes Luís Neubauer de Amorim is a good paper about allosteric effects too. If you wish some help with PCA analysis, just say that I can send to you some scripts that I wrote to perform this analysis with gromacs tools!
- Badges
- Science topic