Hello,
The "bad periodicity" actually corresponds to an evaluation of a dihedral
term, in which the periodicity is only allowed to be integral values 1, 2,
3, 4, or 6. If it's not one of these values, the error message gets
thrown. I'll have to look into why this is actually getting thrown
(possibly a round-off error... I'm not sure, a nab developer would be able
to tell more easily I'm guessing).
Another thing that may be going wrong with your calculation is that you're
running out of available memory. NMODE calculations can be very memory
intensive, and if you're running 3 threads on the same machine without
around 8 GB of memory, it's quite possible that mmpbsa_py_nabnmode is simply
running out of RAM for the calculations. My suggestion is to start a single
nmode calculation with the nab program (you can use MMPBSA.py serial version
for this) and take a look at the memory usage. Can your computer handle 3x
that amount of memory usage?
Good luck!
Jason
On Tue, Aug 31, 2010 at 8:31 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> The snapshots were correctly minimized. Unfortunately, that warning message
> can be misleading. The entropy calculation in MMPBSA.py is done with a nab
> program mmpbsa_py_nabnmode. The issue you are having (with "bad
> periodicity") is an error message invoked by nab, not MMPBSA.py. Possibly a
> nab developer could help with this error message?
>
> -Bill
>
>
> On Tue, Aug 31, 2010 at 8:14 AM, Nicolas SAPAY <
> nicolas.sapay.cermav.cnrs.fr
> > wrote:
>
> > Hello,
> >
> > I'm trying to estimate the binding free energy of a ligand on a protein
> > using the MM/PBSA method and I have difficulties with the calculation of
> > the entropy component with MMPBSA.py. I'm using the following input file:
> >
> > &general
> > verbose=1,
> > startframe=1, endframe=4000, interval=10,
> > /
> > &nmode
> > nmstartframe=1, nmendframe=400, nminterval=100,
> > drms=0.0001, maxcyc=100000
> > /
> >
> > So, I'm calculating the entropy from only 4 snapshots, but it's only to
> > test my scritps. I run the following command lines:
> >
> > export AMBERHOME=/home/software/amber10
> > export PYTHONHOME=/home/software/python-2.7
> > export PYTHONPATH=/home/software/python-2.7/lib/python-2.7
> >
> > amberdir=/home/software/amber11/exe
> > r_free=protein_free
> > l_free=ligand_free
> > md=docking
> >
> > echo "$md"
> > echo "------------------------------------"
> > echo "Start MM/PBSA calculation: `date`"
> >
> > mpirun -np 4 $amberdir/MMPBSA.py.MPI\
> > -O -i mmpbsa.in -o $md.dat\
> > -sp "$md"_solvated.prmtop -cp $md.prmtop\
> > -rp $r_free.prmtop -srp "$r_free"_solvated.prmtop\
> > -lp $l_free.prmtop -slp "$l_free"_solvated.prmtop\
> > -y "$md"_solvated.mdcrd -yr "$r_free"_solvated.mdcrd -yl
> > "$l_free"_solvated.mdcrd
> >
> > echo "End MM/PBSA calculation: `date`"
> > echo "------------------------------------"
> > echo ""
> >
> > First, you can see that I'm using MMPBSA.py.MPI from Amber11 and sander
> > from Amber10. This is because I only have a license for Amber10. Second,
> > I'm not using the default Python distribution (2.4.3) because it was not
> > compatible with MMPBSA.py (MPI4PY actually). I had to install Python 2.7,
> > then MPI4PY and finally MMPBSA.py. Third, you can notice that I'm using 3
> > trajectories to estimatethe free energy: 1 for the solvated complex, 1
> for
> > the solvated protein and 1 for the solvated ligand.
> >
> > With this configuration, the entropy calculation fails with the following
> > errors:
> >
> > Starting nmode calculations...
> > master thread is calculating 1 frames
> >
> > calculating complex for frame number 0
> > bad periodicity: 6
> > bad periodicity: 6
> > bad periodicity: 6
> > calculating receptor for frame number 0
> > bad periodicity: 6
> > bad periodicity: 6
> > bad periodicity: 6
> > calculating ligand for frame number 0
> > bad periodicity: 6
> > bad periodicity: 6
> >
> > Calculations complete. Writing output file(s)...
> > Warning: No snapshots for nmode minimized within tolerable limits!
> Entropy
> > not calculated.
> >
> > For the "bad periodicity" error, I didn't find any explanation about it
> in
> > the manual or the mailing list. For the minimization problem, it seems
> > that the 4 snapshots are actually minimized correctly, as stated in the 3
> > _MMPBSA_xxx_nm.out files. For each snapshot, I can see "----Convergence
> > Satisfied----" at the end of the calculation with the energy correctly
> > minized. So, nmode should be happy with that and perform the normal modes
> > calculation. Does someone understand what happens exactly?
> >
> > Regards,
> > Nicolas
> >
> > --
> > [ Nicolas Sapay - Post-Doctoral Fellow ]
> > CERMAV - www.cermav.cnrs.fr
> > BP53, 38041 Grenoble cedex 9, France
> > Phone: +33 (0)4 76 03 76 44/53
> >
> >
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Aug 31 2010 - 06:00:05 PDT
