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

From: <wmsmith.uci.edu>
Date: Mon, 9 Sep 2013 10:13:26 -0700

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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>
>



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Received on Mon Sep 09 2013 - 10:30:02 PDT
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