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
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Received on Sat Jun 12 2010 - 14:00:03 PDT
