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
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Received on Sat Jun 12 2010 - 15:00:03 PDT
