Hi everyone:
I am calculating normal mode entropy using amber11.
System info:
342 residues protein
1 ligand
Below is my input file:
___________________________________________
Input file for running entropy calculations using NMode
&general
startframe=4001, endframe=5000, keep_files=2, interval=10,
/
&nmode
nmstartframe=1,
nminterval=10, nmode_igb=1, nmode_istrng=0.1,
/
# Execute the program
mpirun -np 8 MMPBSA.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp A-WFE-sol.prmtop -cp A-WFE-nw.prmtop -rp A-nc.prmtop -lp wfe.prmtop -y A-WFE-sol-md9.mdcrd > progress.log 2>&1 &
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Output file:
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Running MMPBSA.MPI on 8 processors...
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home/Amber/amber11/bin/ptraj
nmode program found! Using /home/Amber/amber11/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
100 frames were read in and processed by ptraj for use in calculation.
Beginning nmode calculations with mmpbsa_py_nabnmode...
Master thread is calculating normal modes for 2 frames
calculating complex contribution for frame 0
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
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
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
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
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 :
===============================================
Reading parm file (A-WFE-nw.prmtop)
title:
mm_options: ntpr=10000
mm_options: diel=C
mm_options: kappa=0.103951911959
mm_options: cut=1000
mm_options: gb=1
mm_options: dielc=4.0
mm_options: temp0=298.15
mm_options: wcons=0
scaling charges by 0.500
iter Total bad vdW elect nonpolar genBorn frms
ff: 0 6230417012595346944821921232222945280.00 1678292.63 6230417012595346944821921232222945280.00 -69535.11 0.00 -111.95 3.65e+38
________________________________________________________________
MIN: It= 0 nfunc= 1 E= 6230417012595346944821921232222945280.00000 ( 3.65e+38)
CG: It= 3 ( 0.001)q :-)
LS: i= 1 lhs_f= -3.6909588e+36 rhs_f= -5.8070789e+32
lhs_g= 2.1955886e+36 rhs_g= 5.226371e+36
LS: step= 1 it= 1
MIN: It= 1 nfunc= 5 E= 2539441597772510129576161609305292800.00000 ( 1.38e+38)
CG: It= 1 (999.999)q :-((
LS: i= 1 lhs_f= -1.4970485e+36 rhs_f= -2.3477617e+32
lhs_g= 8.9439214e+35 rhs_g= 2.1129855e+36
LS: step= 1 it= 1
MIN: It= 2 nfunc= 8 E= 1042327953959392618393314531324461056.00000 ( 5.25e+37)
CG: It= 0 (999.999)q :-((
LS: i= 1 lhs_f= -1.0383955e+36 rhs_f= -1.6128561e+35
lhs_g= 7.6150276e+72 rhs_g= 4.1582959e+79
LS: step= 3.490782e-41 it= 1
MIN: It= 3 nfunc= 10 E= 2442916330927895292876510610849792.00000 ( 1.95e+34)
CG: It= 3 ( 0.083)q :-)
LS: i= 1 lhs_f= -1.3877588e+33 rhs_f= -2.1772565e+29
lhs_g= 8.3000993e+32 rhs_g= 1.9595308e+33
LS: step= 1 it= 1
Please anybody could help me understand what is going on and help giving solution to this issue?
Thanks
Shifeng Chen
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Received on Mon Dec 10 2012 - 08:30:02 PST
