Re: [AMBER] Different MMPBSA results in the use of sander and pmemd

From: ǧǧѰ <qianyuqianxun88.gmail.com>
Date: Wed, 11 Sep 2013 21:16:23 +0800

Thank you,Jason
I will check the advices that you hve mentioned one by one.
I have a question here. In the MMPBSA results, what the value of standard
deviation and standard error of the mean can explain?

amy


2013/9/10 Jason Swails <jason.swails.gmail.com>

> On Mon, Sep 9, 2013 at 11:44 PM, ǧǧѰ <qianyuqianxun88.gmail.com> wrote:
>
> > 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?
> >
>
> No, it is probably not enough. That said, there may not be enough time for
> the trajectories to diverge that much, either.
>
> Have you visualized the trajectories to see how different they appear? You
> should not try to discriminate based on MM/PBSA results, since they can be
> misleading. How do the RMSDs compare? How do they compare to each other?
> Perhaps run decomposition per-residue in MMPBSA.py and compare the residue
> contributions for each trajectory and see which residues differ the most.
> Then focus your investigations on those residues to see if they're doing
> anything interesting.
>
> These are all useful questions to ask yourself when investigating something
> curious like this. (Also look at your standard deviation and standard
> error of the mean -- if they overlap between the two trajectories then they
> cannot be discriminated between statistically).
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Sep 11 2013 - 06:30:03 PDT
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