On Tue, Jun 11, 2013 at 4:51 AM, BERGY <nucleic81.gmail.com> wrote:
> Dear Jason,
> The peptide contains Glycine at N-terminal and Glutamate in C-terminal
> When i try for G to A i get the followoing error. i have attached the file
> for u o reproduce
>
> #MMPBSA.py -O -i test_mmpbsa_GB_PB_AlanineScan_together.in -o
> test_mmpbsa_GB_PB_AlanineScan_together_mutantA.out -sp
> renamed_complex-wat_gptieevd.top -cp renamed_complex_gptieevd.top -rp
> renamed_receptor_gptieevd.top -lp renamed_ligand_gptieevd.top -y
> test.mdcrd -mc renamed_T_C70Acomplex.top -ml renamed_T_C70Aligand.top
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /usr/soft/amber12/bin/mmpbsa_py_energy
> cpptraj found! Using /usr/soft/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> Mutating trajectories...
> MutateError: You are trying to mutate GLY to ALA! Not currently supported.
> Exiting. All files have been retained.
>
Glycine to alanine mutations are not supported because this is not a
reduction in the size of the side chain. The way alanine scanning works in
MMPBSA.py is to remove 'extra' atoms and scale the bond lengths of the new
heavy-atom--hydrogen bonds to the equilibrium value. It does not have any
code to add atoms, so we don't support GLY->ALA mutations.
> ---------------------------------------------------------------------------
>
> When i try for D to A
> i get the following error
>
> #MMPBSA.py -O -i test_mmpbsa_GB_PB_AlanineScan_together.in -o
> test_mmpbsa_GB_PB_AlanineScan_together_mutantH.out -sp
> renamed_complex-wat_gptieevd.top -cp renamed_complex_gptieevd.top -rp
> renamed_receptor_gptieevd.top -lp renamed_ligand_gptieevd.top -y
> test.mdcrd -mc renamed_T_C70Hcomplex.top -ml renamed_T_C70Hligand.top
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /usr/soft/amber12/bin/mmpbsa_py_energy
> cpptraj found! Using /usr/soft/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> Mutating trajectories...
> IndexError: list index out of range
>
This would be a problem, I'll look into it.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jun 11 2013 - 06:00:03 PDT
