hello, thank you for your reply. I have two different trajectories, one is
done in sander, and the other in pmemd.I can get Jason's point. Maybe the
two simulations could be exploring completely different regions of phase
space.
But in my system,the ligand binding to the protein has a Crystal Structure,
I just want it to reach an equilibrium state. I think the Crystal Structure
is stable,so i simulation 1ns in sander and pmemd, do you think it is
enough?
2013/9/10 <wmsmith.uci.edu>
> Hello,
> As far as I can see, using radiiopt = 0 gives the same results for both
> Amber12 and Amber13 under pbsa when I use the same mdcrd and paramater
> files you sent. Using radiopt=1 does seem to vary slightly. I'm not sure
> exactly why, but the deviation is very small.
> Also, I only saw one coordinate trajectory file in the zip you sent
> though. Were there 2 different trajectories? If you are comparing two
> separate runs, then as Jason said, slightly different results are
> expected. Particularly if you haven't run long enough to achieve good
> convergence.
> -Wes
> > On Mon, Sep 9, 2013 at 5:49 AM, ǧǧѰ <qianyuqianxun88.gmail.com>
> > wrote:
> >
> >> Hi,everyone
> >>
> >> I have used MMPBSA.py to calculate the binding erergy of a complex which
> >> includes a protein and a ligand .For a same complex,I use the same
> >> inputfilein sander and
> >> pmemd programme at the equilibrium stage.Then I use the mdcrd file to
> >> begin
> >> MMPBSA. But the results of GB are quite different. The difference value
> >> is
> >> 22 kcal/mol.
> >> Have you met this question? I have several questions
> >> 1, the process which i use is right?
> >> 2, what is the reason of the D-value?
> >>
> >
> > You may not have run long enough to obtain converged results. The
> > trajectories of 2 simulations will never be identical with different
> > programs, but that doesn't make one of them 'wrong', just 'different'
> > (i.e., the two simulations could be exploring completely different
> regions
> > of phase space).
> >
> > However, there is so little information here that we cannot possibly
> > provide specific help or advice. pmemd and sander have been so
> thoroughly
> > evaluated and checked that I find it highly unlikely that 'standard' MD
> in
> > either program is 'wrong'.
> >
> > Also, you should not be analyzing the 'equilibration' dynamics, since the
> > equilibration stage is typically non-equilibrium. (It is probably better
> > termed the 'relaxation' stage) You should run at least 5 to 10 ns of
> > simulation AFTER a multi-nanosecond equilibration/relaxation stage before
> > attempting MM/PBSA.
> >
> > Good luck,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
>
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Received on Mon Sep 09 2013 - 21:00:05 PDT
