I am trying to simulate a protein bound to a ligand but I can't see the point of convergence in the RMSD plot. The protein I am using has some chains missing. Could that be the cause?
Without seeing the plot, it's hard to say. Missing chains may not be a big deal, unless the missing chains are proteins or other molecules that stabilize the one you're simulating. If you're missing parts of chains (residues) then yes, this can be a problem, depending on what's missing. Missing internal residues must be rebuilt. Missing terminal residues are usually less of an issue.
Another issue is time. How long was your simulation? If the simulation is short, then perhaps there just hasn't been time for the RMSD to stabilize.
The RMSD also depends on the structure; if the protein has lots of loops, the RMSD may never really converge, but this also doesn't tell you much of use. Calculating the RMSD of the formed secondary structure elements can be useful in this case.
Without seeing the plot, it's hard to say. Missing chains may not be a big deal, unless the missing chains are proteins or other molecules that stabilize the one you're simulating. If you're missing parts of chains (residues) then yes, this can be a problem, depending on what's missing. Missing internal residues must be rebuilt. Missing terminal residues are usually less of an issue.
Another issue is time. How long was your simulation? If the simulation is short, then perhaps there just hasn't been time for the RMSD to stabilize.
The RMSD also depends on the structure; if the protein has lots of loops, the RMSD may never really converge, but this also doesn't tell you much of use. Calculating the RMSD of the formed secondary structure elements can be useful in this case.
- Badges
- Science topic