Dear Jason,
Thanks for your information.
My system is a homodimer. So if I mutate one residue in one monomer, I
should mutate the corresponding one in the other monomer.
But as you said, the mutant is independent. Maybe mutating one residue
is OK.
I will try the decomposition capability in mm_pbsa.pl and thanks for
your suggestion.
Best Regards,
Zhijian Xu
Jason Swails wrote:
> Hello,
>
> The idea was that you would want to know the contributions independently,
> anyway, so you'd have to run 2 simulations (one for each mutant).
> Ultimately, the alanine scanning technique has not seen much use in our
> experience because of the decomposition capability, which can be used to
> give similar information (but is not available through MMPBSA.py and
> amber9).
>
> All the best,
> Jason
>
> On Thu, Dec 9, 2010 at 7:45 AM, zjxu <zjxu.mail.shcnc.ac.cn> wrote:
>
>
>> Dear Bill,
>> Thanks for your reply. Now I get it.
>>
>> Best Regards,
>> Zhijian Xu
>>
>> Bill Miller III wrote:
>>
>>> Your assumption would be correct. A current limitation of the alanine
>>> scanning function in MMPBSA.py is that it can only accept one mutant at a
>>> time.
>>>
>>> -Bill
>>>
>>> On Thu, Dec 9, 2010 at 2:31 AM, zjxu <zjxu.mail.shcnc.ac.cn> wrote:
>>>
>>>
>>>
>>>> Dear everyone,
>>>> I have a dimer composed of Chain B and Chain C (both chains were defined
>>>> as receptor and ligand separately), and I want to use alanine scanning
>>>> to asses the contribution to the dimer formation of some residues reside
>>>> on the dimer interface.
>>>> Firstly, I use the newest version of the MMPBSA.py. When I mutate 2
>>>> resides (one in receptor and one in ligand), then error happed as below:
>>>> MMPBSA.py -i mmpbsa.in -o mmpbsa.out -sp ../B_C.prmtop -cp
>>>> ../B_C_pr.prmtop -rp ../B_pr.prmtop -lp ../C_pr.prmtop -y ../md6-10.crd
>>>> -mc B_C_mut.prmtop -mr B_mut.prmtop -ml C_mut.prmtop
>>>> ptraj found! Using /home/zjxu/project/prog/amber9/exe/ptraj
>>>> sander found! Using /home/zjxu/project/prog/amber9/exe/sander
>>>> Assuming /home/zjxu/project/prog/amber9/exe/sander is part of
>>>> amber9 or amber10. Using old PB input file.
>>>> Warning: igb=5 should be used with either mbondi2 or bondi pbradii set.
>>>> Yours are modified Bondi radii (mbondi)
>>>> Checking mutant topology files...
>>>> Error: More than one mutated residue!
>>>> Error: Invalid alanine scanning topology file(s)!
>>>> NOTE: All files have been retained for debugging purposes. Type
>>>> MMPBSA.py --clean to erase these files.
>>>>
>>>> However, when I mutate just one residue, then the process can be
>>>> completed rightly.
>>>> And I tried mm_pbsa.pl when mutate 2 residues, and everything is OK.
>>>> So I have a doubt that could MMPBSA.py mutate more than 1 residue?
>>>>
>>>> I used amber9 and have applied all the patches for amber9 and MMPBSA.py.
>>>> The mmpbsa.in for MMPBSA.py is as below:
>>>> sample input file for running alanine scanning
>>>> &general
>>>> startframe=1, endframe=5000, interval=5,
>>>> verbose=1,
>>>> /
>>>> &gb
>>>> saltcon=0.1
>>>> /
>>>> &pb
>>>> istrng=0.100
>>>> /
>>>> &alanine_scanning
>>>> /
>>>>
>>>> thanks for your time
>>>> Best Regards,
>>>> Zhijian Xu
>>>>
>>>>
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>>
>>>
>>>
>>>
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>
>
>
>
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Received on Thu Dec 09 2010 - 18:30:05 PST
