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
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Received on Sat Jun 12 2010 - 13:30:05 PDT
