On Thu, Aug 1, 2013 at 4:44 PM, George Green <soyo.green.gmail.com> wrote:
> Ok, I'm now getting a really weird problem that has got me scratching my
> head. If I take the decomposition parameters out of the mmpbsa.in file,
> the
> script fails with the following error:
>
> ----------------------------------------
> File "/apps/applications/amber/12/1/default/amber12/bin.real/MMPBSA.py",
> line 565, in ?
> external_progs, '_MMPBSA_', normal_system)
> File
>
> "/apps1/applications/amber/12/1/default/amber12/bin/MMPBSA_mods/calculation.py",
> line 176, in run_calculations
> calc.Run()
> File
>
> "/apps1/applications/amber/12/1/default/amber12/bin/MMPBSA_mods/calculation.py",
> line 664, in Run
> raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> CalcError:
> /apps/applications/amber/12/1/default/amber12/bin/mmpbsa_py_energy failed
> with prmtop
>
> ../../../../ALA_Complex_mmpbsa_leap/ProtLigOnly_mmpbsa_ALA_Bound_mbondi.parm!
>
Is this the whole stderr stream? It would help to have the output and
error streams, since the error message might be in one of those.
>
>
> Exiting. All files have been retained.
> ----------------------------------------
>
>
>
> The _MMPBSA_complex_pb.mdout.0 file has the following info:
> [snip]
>
>
> The mmpbsa.in file is as follows:
> -----------------------------------------------------
> #Sample input file for GB and PB calculation
> &general
> startframe=1, endframe=4000, interval=2000,
> verbose=2, keep_files=0, debug_printlevel=3,netcdf=1,
> /
>
> &pb
> istrng=0.15, fillratio=4.0,
> cavity_offset=0.92, cavity_surften=0.00542,
> exdi=80.0, indi=1.0,
> radiopt=1,
>
>
> /
>
radiopt=1 means use optimized radii. There are quite a few cases where
this does not work because some of your atom types may not be supported by
this model. Setting radiopt=0 often fixes this issue. But this diagnosis
is pure speculation since your output files didn't have enough information
to help me.
Also make sure that your AmberTools 13 is fully up-to-date.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 01 2013 - 14:30:04 PDT
