Hi Amor,
Find the attached tutorial
Best,
Hirdesh
On Fri, Sep 24, 2010 at 12:10 PM, Amor San Juan <amorsanjuan.yahoo.com>wrote:
> 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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>
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Received on Fri Sep 24 2010 - 00:00:11 PDT
