On 30/07/2012 3:39 AM, tarak karmakar wrote:
Dear All,
In my initial protein pdb structure I have added some external ligand
molecules and as a result of that there are several short contacts.
So, well, I minimized the system and then got the 'prot_min.gro' file.
Now after the equilibration run, I plotted the RMSD of the resulting
trajectory with respect to the initial pdb structure. So as the pdb
had some short contacts, the resulting RMSD is showing large
increasing value around 0.4-0.5 nm.
1) Then, is it better to plot [ for reporting purpose ] the RMSD of
the trajectory with respect to the minimized coordinate file rather
than w. r. t. the initial PDB file?
Since neither of those configurations were sampled from the target
ensemble, it's a bit hard to say they make good reference states. Doing
initial MD with position restraints on the protein stops it moving much
while the ligand gets sorted out. Use that as the reference state from
which you begin production MD.
Better still, stop and consider how you will analyse your results before
you begin your simulation. Then you're better placed to do a simulation
that will lead to a meaningful result.
2) What is the acceptable range of RMSD for a protein simulation ? (
below 0.2 nm !! )
It depends on a whole host of things. There's no magic number.
Mark
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