Dear Jason,
Any update on the problem that i had reported. I am waiting for your reply
as the reviewer's are questioning why i could not do the mutation on the
c-terminal peptide residue.
In the previous emails, I had sent u the files to debug, as per ur request.
Thanking you
bergy
On Tue, Jun 11, 2013 at 6:04 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
>
> 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 Jul 23 2013 - 01:00:03 PDT
