Thanks.
On Sat, Jun 12, 2010 at 3:06 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Shenna
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Received on Sat Jun 12 2010 - 16:30:04 PDT
