AMBER Archive (2008)

Subject: Re: AMBER: mm-pbsa multiple trajectory approach?

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Wed Apr 02 2008 - 16:18:06 CDT

The energy numbers are what they are - and there will be lots of
statistical noise in them, in my experience.

You can directly import the MM-PBSA output into an spreadsheet quite
easily - and manipulate it from there for the different trajectories.

So, I think it should be very easy to duplicate the single-trajectory
PERL script math this way.

An easy test ought to be to take the tutorial, make three "receptor
only" variants, load those into a spreadsheet and duplicate the math of
the single-shot tutorial.

Again, apologies in advance if I fundamentally do not understand what
you are trying to do.

Seth Lilavivat wrote:
> Chris,
>
> 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.
>
> Thanks,
> Seth
>
> On 3/26/08, *Chris Moth* <chris.moth_at_vanderbilt.edu
> <mailto:chris.moth_at_vanderbilt.edu>> 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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