On Thu, Oct 6, 2011 at 7:09 PM, Irene Newhouse <einew.hotmail.com> wrote:
>
> I'm reproducing [because I want to compare the results to another system]
> previously published work on a cytochrome C- neuroglobin complex. The
> protein-protein docking was done with freeware & that work didn't require a
> scoring function outside the one that came with that software. However, I'm
> thinking of equilibrating the structure from the docking software with MD &
> using MMPBSA to compute the delta G of interaction for this system as well
> as the one I want to compare to it. I have an input pdb structure arranged
> as cytochrome coords-TER-cytochr. heme-TER-neurgl-TER-neur heme. I've also
> tried it w/out the TER between globin & its respective heme, with identical
> results. I can easily use sleap to create a prmtop/inpcrd set. However,
> when I try to use ante-MMPBSA using a receptor_mask ":1-105" I get an error
> message regarding the C-terminal residues on each of the globin proteins.
> The error is that there's an extra OXT in each C-terminal residue. I suspect
> this may be because residue 105 is the heme & residue 104 is the C-terminal
> protein residue. I'm not at all interested in the protein/heme part of the
> interaction; I want the globin/globin interaction. Since the edges of the
> hemes are close to each other in the docked pose, I can't just ignore them.
> Is there a way to set this up with MMPBSA?
>
You can't use ante-MMPBSA.py to create your topology files. It was a (in my
opinion) rather clumsy experiment to see if the process of creating
compatible topologies could be automated via just the information in the
largest topology file you used (it should theoretically be possible since
all of the information is *there*). It suffers several limitations, though.
The most serious one (and the one that you found) is that the
identification of N- and C-termini are hard-coded to be the first and last
non-solvent residues, respectively. Therefore, any dimer with internal
charged termini will suffer this error.
I've just finished a prmtop editing utility (to be released with the next
AmberTools version) that takes a much better approach -- it can delete atoms
directly from a topology file without having to go through leap, thereby
guaranteeing that this will work for any system*. ante-MMPBSA.py will use
this new approach in the future. Until then, though, you'll have to
construct your topology files the old way :).
HTH,
Jason
As an aside, I didn't think anybody (me included) actually *used*
ante-MMPBSA.py. Is this true?
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Oct 06 2011 - 17:30:03 PDT
