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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 24 2010 - 00:00:09 PDT
