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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>>
>>
>
>
>
>
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Received on Thu Dec 09 2010 - 05:00:03 PST
