AMBER Archive (2004)

Subject: Re: AMBER: PBCAL in mmpbsa

From: nlxc (
Date: Tue Jun 29 2004 - 19:29:51 CDT

 Thanks a lot. Based on the curve of EPTOT vs. time and DENSITY vs.
time, my system looks well equilibrated. Do I have to run production MD
under NVT condition or I still can use NPT for my production run. Is there any
standard such as rmsd for how well the system is equilibrated?

Thanks a lot for help!


Thomas Steinbrecher <> wrote:Hi Nan,

>a little surprise to me since the PBCAL values for the same receptor in
>those two systems( through separate MD and mm/pbsa) have about 40 Kcal
>difference(std=22), and the ligand also has 1.5 difference(std=1). What
>could be the possible reasons to make the PB values of two exactly same
>receptors so different?

I have noted that even small differences in starting geometries
can result in quite different deltaG results from MM-PBSA.
This is probably only more true if you study two similar ligands instead
of two conformations of one ligand.
But still, 40kcal/mol difference sounds like something else is going
on. Are you sure your simulation is well equilibrated? You mentioned that
your crystal structure does not have a ligand bound to it, so maybe the
geometry of the binding site is far from equilibrium with the ligand



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