My WT complex was simulated for about 40ns. I took a snapshot from the last
5ns of data and created 3 complexes in pdb format. I manually modified one
of the complex structures and using leap I created six gasphase topology and
coordinate files for the complex, receptor and ligand. I already have a
solvated complex. I ran MMPBSA in parallel and serial. I looked into one of
the _MMPBSA.mdout files and I saw that for BOND and VAADWL stars(****)
appear. I am not sure if that means I need to recreate my topology and
coordinate files because they are corrupted or do I need to simulate the
complex a little longer. Any suggestions, please? Thanks.
On Wed, Jun 9, 2010 at 1:52 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Jun 9, 2010 at 4:44 PM, shenna shearin <smsheari.gmail.com>
> 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/MMPBSA.py.MPI -O -i
> > mmpbsa.in -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!
> Jason
>
>
> >
> > Gracie
> > smsheari.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Shenna
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Received on Sat Jun 12 2010 - 13:30:03 PDT
