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
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Received on Tue Aug 31 2010 - 06:00:03 PDT
