Hi everyone:
I am calculating normal mode using amber11 using mmpbsa.py.
System info:
199 residues protein
1 ligand
5 waters
Below is my input file:
___________________________________________
MMPBSA.py input file for running GB
&general
verbose=2, strip_mdcrd=0,
/
&nmode
nmstartframe=1, nmendframe=181,
nminterval=5, drms=0.00001,
maxcyc=1000000, ala_entropy=1,
nmode_istrng=0.100, nmode_igb=1,
/
EOF
# Execute the program
$DO_PARALLEL $EXE -O -i mmpbsa.in \
-cp ../../5wat.prmtop \
-rp ../../plW5.prmtop \
-lp ../../pep.prmtop \
-y ../../x.mdcrd
-o FIN.out
_________________________________________________
Output file:
_________________________________________________
ptraj found! Using /usr/local/amber11/bin/ptraj
sander found! Using /usr/local/amber11/bin/sander
nmode program found! Using /usr/local/amber11/bin/mmpbsa_py_nabnmode
Preparing trajectories with ptraj...
188 frames were read in and processed by ptraj for use in calculation.
Starting calculations...
Starting nmode calculations...
master thread is calculating 37 frames calculating receptor for frame number 1
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
Line minimizer aborted: step at lower bound
____________________________________________
_MMPBSA_complex_nm.out output file (just bottom of file):
===============================================
----Convergence Satisfied----
iter Total bad vdW elect nonpolar genBorn frms
allocation failure in vector: nh = 33506892
===============================================
_MMPBSA_complex_nm.out output file (just bottom of file):
===============================================
LS: i= 6 lhs_f= 4.0971986e-07 rhs_f= -8.1134712e-18
lhs_g= 0.001653204 rhs_g= 0.0014878838
LS: i= 7 lhs_f= 4.0965233e-07 rhs_f= -2.677781e-25
lhs_g= 0.0016532042 rhs_g= 0.0014878838
LS: i= 8 lhs_f= 4.0965233e-07 rhs_f= -1.6532042e-27
lhs_g= 0.0016532042 rhs_g= 0.0014878838
LS: step= 1e-20 it= 8
===============================================
Please anybody could help me understand what is going on and help give solution to this issue?
Thanks
Amor
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Received on Fri Sep 24 2010 - 00:00:09 PDT
