Antonio, can you tell us more details? which coordinates and prmtop (in
terms of # waters) were used for the sander input inpcrd and prmtop? which
coordinates (again, # waters) were used for the refcrd? did the MD use the
original or the edited prmtop?
even though there are 2 systems, what's most important is the pairing of
the prmtop and inpcrd. the refcrd is less important since it is a reference
and not actually used to perform MD.
On Mon, Dec 22, 2014 at 12:43 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> 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 - 10:00:03 PST
