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
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Thu Dec 09 2010 - 04:00:04 PST
