On Fri, Apr 17, 2015 at 4:38 AM, maryam azimzadehirani <
maryamai1988.gmail.com> wrote:
> Hi Jason,
> I am using amber12. I have tried this input file:
> Input file for running PB and GB
> &general
> endframe=100, verbose=1,
> debug_printlevel=2
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.00
> /
> &pb
> istrng=0.00,
> inp=1,
> radiopt=0
> /
> &alanine_scanning
> /
> #/usr/local/packages/amber12/bin/MMPBSA.py -O -i mmpbsa.in -sp
> ras-raf_solvated.prmtop -cp rasraf.prmtop -rp ras.prmtop -lp raf.prmtop -y
> *.mdcrd -mc rasraf_mutant.prmtop -mr ras_mutant.prmtop
>
> I got this argument:
>
> cpptraj found! Using /usr/local/packages/amber12/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> Mutating trajectories...
> File "/usr/local/packages/amber12/bin/MMPBSA.py", line 527, in <module>
> str(external_progs['cpptraj']), normal_system, mutant_system)
> File "/usr/local/packages/amber12/amber12/bin/MMPBSA_mods/make_trajs.py",
> line 318, in make_mutant_trajectories
> norm_sys.complex_prmtop, mut_sys.complex_prmtop)
> File "/usr/local/packages/amber12/amber12/bin/MMPBSA_mods/alamdcrd.py",
> line 175, in __init__
> self.mutres = self.FindMutantResidue()
> File "/usr/local/packages/amber12/amber12/bin/MMPBSA_mods/alamdcrd.py",
> line 210, in FindMutantResidue
> self.orig_prm.prm_name))
> TypeError: not all arguments converted during string formatting
> Exiting. All files have been retained.
>
> Is it caused because of the version of Amber tools I am using?
>
No, this bug was in the current development version (but I just fixed
it). As I suspected, the bug was present when trying to report an error.
In particular, this was the error message that was *supposed* to be printed:
raise MutateError('Your mutant prmtop (%s) has the same sequence '
'as the original!' % self.new_prm.prm_name)
So your mutant prmtop and non-mutant prmtop for the complex has exactly the
same sequence (maybe the residue you tried converting to ALA was already an
ALA?)
I hope this helped and thanks for the report,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Apr 17 2015 - 05:00:04 PDT
