On Mon, 2014-12-22 at 15:37 +0100, antonio.coluccia.uniroma1.it wrote:
> Dear Dr. Simmerling
> I have computed the RMSD value with Maestro.
> The reference structure that i use is the activated conformation of the
> protein .
> My idea is to try to compute the trajectory from the inactive (X-ray
> structure) to active conformation (X-ray structure) looking for the
> most moving residues. Despite are two conformations of the same protein
> one (active) is "larger" that the other, indeed the inactive was
> solvatated with 46879 water molecules and the active one with 69302.
> Thus, to have the same number of atoms i have stripped by parmed the
> excess water molecules, does could it affect the water box integrity?
Yikes. This is a HUGE difference in the number of water molecules.
ParmEd (or cpptraj) will spit out a *correct* topology file, in that it
will run and give energies. However, neither one will compress the box
of the system you removed the waters from. As a result, your density
will be way too low for the active system and it will vigorously boil.
It will probably take a very long time for your system size to
equilibrate to standard conditions using constant pressure MD.
The trick you used is a good one to force two systems to have the same
number of water molecules, but you should try very hard to get the
starting numbers of waters as close as possible before deleting any so
that you do not have to delete more than a few dozen waters. Otherwise
your density will be too low.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 22 2014 - 10:00:02 PST
