Re: AMBER: mm-pbsa multiple trajectory approach?

From: Seth Lilavivat <>
Date: Fri, 28 Mar 2008 11:28:31 -0400


I get what you are saying. I know that you don't have to make any changes to
output on "complex" or "receptor" only. For my config file, I simply specify
that there is 1 receptor, 0 complexes, and 0 ligands. However, it is still
unclear if there is a way to take the energy difference between two
structures if they are in different trajectories.


On 3/26/08, Chris Moth <> wrote:
> A nice thing I recall about the mm-pbsa script in the AMBER suite is that
> it is a very transparently written PERL script. So, you should feel
> comfortable opening the file, and making small changes.
> I am not in front of our source now - but I recall from a few years ago
> that you could ask for output on "complex" or "receptor" only - and it
> would give output. Otherwise, if it is not that easy, I don't think the
> PERL script modifications are going to be very great for you.
> And, if the response above makes no sense whatsoever in the context of
> your version of AMBER, accept my apologies in advance!
> Chris
> > Dear Amber users,
> >
> > I am using mm-pbsa as in a similar way to the tutorial except that I am
> > using multiple trajectories (one for the complex, one for the ligand,
> and
> > one for the receptor). Is there a way to get mm-pbsa to calculate the
> > statistics in one shot like in the single trajectory example?
> >
> > Thanks,
> > Seth
> >
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Received on Fri Apr 18 2008 - 21:14:47 PDT
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