Re: [AMBER] MMPBSA error

From: Ray Luo, Ph.D. <ray.luo.uci.edu> Date: Thu, 10 Oct 2013 14:30:35 -0700

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Thu, Oct 10, 2013 at 12:36 PM, Symon Gathiaka
<smg0020.tigermail.auburn.edu> wrote:
> Dear Amber users,
>
> I am using the MMPBSA.py.MPI on a protein with a modified amino acid and the log file is giving the following error:
>
> CalcError: /opt/asn/apps/amber12_tools13/amber12/bin/mmpbsa_py_energy failed with prmtop complex.prmtop!
>
> The same calculation for the protein without the modified residue is working!
>
> Furthermore, the _MMPBSA_complex_pb.mdout.0 file is giving the below error:
>
> Reading parm file (complex.prmtop)
> title:
> default_name
>      Parameter topology includes 10-12 terms:
>      These are assumed to be zero here (e.g. from TIP3P water)
>         mm_options:  e_debug=3
>         mm_options:  ipb=2
>         mm_options:  inp=2
>         mm_options:  epsin=1.000000
>         mm_options:  epsout=80.000000
>         mm_options:  smoothopt=1
>         mm_options:  istrng=100.000000
>         mm_options:  radiopt=1
>         mm_options:  dprob=1.400000
>         mm_options:  iprob=2.000000
>         mm_options:  npbopt=0
>         mm_options:  solvopt=1
>         mm_options:  accept=0.001000
>         mm_options:  maxitn=1000
>         mm_options:  fillratio=4.000000
>         mm_options:  space=0.500000
>         mm_options:  nfocus=2
>         mm_options:  fscale=8
>         mm_options:  bcopt=5
>         mm_options:  eneopt=2
>         mm_options:  cutnb=0.000000
>         mm_options:  sprob=0.557000
>         mm_options:  cavity_surften=0.037800
>         mm_options:  cavity_offset=-0.569200
> Error: ipb>0 is incompatible with periodic boundary conditions.
> Error: To use this method set IFBOX in the PRMTOP file to 0.
> Error: See http://ambermd.org/formats.html
>
> Please help for i can not figure the way to deal with it.
>
> Thanks,
> Symon
>
>
>
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