Re: [AMBER] MMPBSA Alanine scan terminal residues

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 23 Jul 2013 08:23:25 -0400

Hi Bergy,

Sorry, this had slipped my mind (I had a particularly busy month). I think
I've fixed the issues with alanine scanning with C- and N-terminal
residues. I've attached an alamdcrd.py file to this email which you should
put inside $AMBERHOME/bin/MMPBSA_mods/

After you put that file in that directory, please see if your problem goes
away (try only one or two frames, and visualize your trajectory). Note,
this is only affecting your installed MMPBSA.py, so do not recompile or the
change will go away.

Thanks!
Jason


On Tue, Jul 23, 2013 at 3:38 AM, BERGY <nucleic81.gmail.com> wrote:

> 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
>>
>
>
-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher



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Received on Tue Jul 23 2013 - 05:30:03 PDT
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