That was the problem. Thanks so much.
On Sat, Jun 12, 2010 at 1:38 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> The appearance of stars typically means that the topology files are
> inconsistent with the coordinate files. You can use a visualization
> program
> (such as VMD) to visualize your coordinate files with your topology files.
> If it doesn't look normal, then they're inconsistent. Make sure you have
> no
> ions or waters in your complex/receptor/ligand topology files, and make
> sure
> that all amino acids have the same protonation states (i.e. ASP or ASH) in
> each topology file that it is in (i.e. complex and receptor or complex and
> ligand).
>
> Good luck!
> Jason
>
> On Sat, Jun 12, 2010 at 4:13 PM, shenna shearin <smsheari.gmail.com>
> wrote:
>
> > My WT complex was simulated for about 40ns. I mutated a residue from the
> WT
> > complex and simulated that structure for 5ns.
> > I took a snapshot from the last 3ns 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 Sat, Jun 12, 2010 at 1:10 PM, shenna shearin <smsheari.gmail.com>
> > wrote:
> >
> > >
> > >
> > > 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
> > >
> >
> >
> >
> > --
> > Shenna
> > _______________________________________________
> > 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 - 14:30:03 PDT
