If you did the calculation on one frame, then the standard deviation and
standard error of mean would be expected to be zero. If you did the
calculation on more than one frame, then either something went wrong of the
energy values are exactly the same for every single frame.
-Bill
On Sat, Jun 12, 2010 at 5:49 PM, shenna shearin <smsheari.gmail.com> wrote:
> In my FINALRESULTS.dat file the Std. dev and Std. error of mean values are
> all zero. Does this indicate an error somewhere?
>
> On Sat, Jun 12, 2010 at 2:13 PM, shenna shearin <smsheari.gmail.com>
> wrote:
>
> >
> > 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
> >
>
>
>
> --
> Shenna
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Sat Jun 12 2010 - 15:30:03 PDT
