Re: [AMBER] MM_PBSA: multiple processes, single point output along the trajecotry and cropped structures

From: Jason Swails <>
Date: Tue, 1 Jun 2010 17:33:16 -0400


I think is the MM/PBSA utility most suited to your needs:
described below. It is available on the amber tutorial websites (see

On Tue, Jun 1, 2010 at 3:55 PM, Yuqin Cai <> wrote:

> Dear AMBER community,
> I am computing free energies for three carcinogen-containing duplexes using
> MM-PBSA. By replacing the carcinogen with a hydrogen atom, i can compare
> the
> distortion each carcinogen causes to the B-DNA duplex. Here are my
> questions:
> 1) how to use multiple processes, especially during delphi? For an 800
> atom
> structure, it took me ~2 weeks to get the average free energy over 5000
> snapshots. I wonder if i could make it faster.

Look at the recent release of This includes an MPI version, which will parallelize across frames, just like you ask for.
You can run this on up to 5000 processors (on 5000 processors, it will run
one frame on each thread). Also, because this uses MPI, if you install
mpi4py (explained on the website above), it will run on any system with a
working MPI. The version of released with amber11 uses a forking
utility to spawn multiple processes to run computations, and I believe this
is restricted to shared memory machines. Thus, you are constrained to as
many processors as you have on a single node. Note that it does not use
delphi, but can use either APBS or PBSA to solve the PB equation (and PBSA
can be made to reproduce delphi numbers with the right input files)

> 2) how to put out the results for each snapshot during the trajectory,
> instead of an overall average, so that I can do a clustering analyses?

This you will have to do on your own, but if you set keep_files = 2 to keep
all relevant files, you can look at the mdout files (_MMPBSA_*.mdout, see
the manual for descriptions), and each block of data corresponds directly
(sequentially) to the frames printed in the _MMPBSA_*.mdcrd files. Thus,
you can cluster these after runs, and it should be fairly easy to
do with simple scripts and grep/awk.

> 3) how to cap the ends if i want to carry out analyses for a cropped
> structure?

Not quite sure what you mean here. See the ACE/NME/NHE caps for use in leap.

Good luck!

> Many thanks,
> Yuqin
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Jun 01 2010 - 15:00:04 PDT
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