Re: [AMBER] MMPBSA binding calculations

From: Jason Swails <>
Date: Wed, 9 Jun 2010 16:52:26 -0400

On Wed, Jun 9, 2010 at 4:44 PM, shenna shearin <> wrote:

> Greetings Amber community:
> I am calculating the binding free energy of a protein-protein complex in
> parallel. I was able to calculate the binding energy of the WT complex with
> no problem but when I tried a mutated complex I encounter problems. I
> created my gas phase and solvated topology and coordinate files as
> directed.
> When I ran the script: mpirun -np 4 $AMBERHOME/bin/ -O -i
> -o FINAL_RESULTS_MMPBSA.dat -sp ras-raf_solvated.prmtop -cp
> ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y *.mdcrd > progress.log 2>&1
> using my own input files the calculation runs smoothly for a while cease.
> In
> the output file 'progress.log' I see an error that states: The files have
> been retained for debugging purposes. Type MMPBSA --clean to erase the
> files. I need clarity on why this is happening and how to retify this
> problem. Can someone please help. Thanks in advance.
You need to give us more information. That was the message that simply
states that the calculation didn't finish successfully. The actual error
message should have come before. What did the log say? If it seems like
there was a problem with the sander outputs, look at some of the files that
end in .mdout (and begin with _MMPBSA_).

You should also run a short simulation with a couple of frames and see if it
works (both in serial and in parallel).

Good luck!

> Gracie
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Wed Jun 09 2010 - 14:00:05 PDT
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