AMBER Archive (2008)

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

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Wed Mar 26 2008 - 17:21:25 CDT

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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