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?
Regards,
Maryam
On Thu, Apr 16, 2015 at 9:33 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> What version of Amber are you running?
>
> Can you set debug_printlevel=2 in the &general section of your input file
> and try running again?
>
> I suspect that the error you are seeing is a mistake I made in creating an
> error message that outlines the *real* problem.
>
> Thanks,
> Jason
>
> On Thu, Apr 16, 2015 at 3:06 AM, maryam azimzadehirani <
> maryamai1988.gmail.com> wrote:
>
> > Dear amber users,
> > I am trying to run alanine scanning with MMGBSA.py. I generated all the
> > complex,ligand,receptor and mutated files together but I get this error
> > after running the job:
> > Loading and checking parameter files for compatibility...
> > mmpbsa_py_energy found! Using
> > /usr/local/packages/amber12/amber12/bin/mmpbsa_py_energy
> > cpptraj found! Using /usr/local/packages/amber12/amber12/bin/cpptraj
> > Preparing trajectories for simulation...
> > Mutating trajectories...
> > *TypeError: not all arguments converted during string formatting*
> > Exiting. All files have been retained.
> >
> > I have looked the mailing list for the similar bugs. Found this one which
> > seems like a similar case to mine
> > http://archive.ambermd.org/201409/0035.html since I also mutated a
> > residue
> > in the ligand. Just couldn’t get the final solution for the error...
> > will be grateful if you advise,
> > Maryam
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Apr 17 2015 - 02:00:02 PDT
