It looks like you have a problem between your coordinate and topology
files. Common things to look out for -- did you keep any waters in your
complex topology. Ions? Do you have any 'strange' ions?
Try visualizing your intermediate trajectories (_MMPBSA_complex.mdcrd,
_MMPBSA_receptor.mdcrd, and _MMPBSA_ligand.mdcrd) with the corresponding
topology files in VMD (or some other visualization program) to see if the
structures look horribly wrong.
Also look at the default strip_mask definition (in the Amber manual). You
may have to modify this if you have 'weird' ions in your system.
Good luck,
Jason
On Mon, Dec 10, 2012 at 11:02 AM, Mu Xia <muxiachuixue.163.com> wrote:
> 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 &
> _________________________________________________
>
>
> Output file:
>
>
> _________________________________________________
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Dec 10 2012 - 09:00:04 PST
