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
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> >
> >
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Dec 09 2010 - 08:00:04 PST
