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
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Received on Tue Aug 31 2010 - 05:30:03 PDT
