I'll just add a little to what Dwight said. The way the mask guessing
function operates is to take the ligand sequence and insert it into each
position of the receptor sequence. A match is detected when this composite
sequence matches the complex, and the masks are chosen based on where the
ligand was inserted.
It starts at the end of the receptor and works its way to the beginning
(since usually the receptor comes first in the sequence and the ligand
comes at the end). This strategy works in the vast majority of cases. And
if this strategy *should* work, but it appears not to, then it is a virtual
certainty that there is something wrong with your topology files (maybe you
forgot to remove ions or waters, wrong tautomeric/protomeric states for
some of your residues, some missing or extra atoms in the unbound states
that are not in the bound state, etc.). The main impetus for adding this
functionality was actually to serve as an error catch to provide a helpful
avenue for debugging (by letting you know that your topology files are
wrong).
Furthermore, it should be obvious when this strategy *won't* work, and when
you need to specify these masks yourself. Examples include:
- There are multiple ligands with the same name, and you don't want to
analyze the one that comes last in the sequence.
- What you call the "ligand" is comprised of multiple residues that are not
continuous in the complex sequence. Perhaps you have a dimer and each
monomer has a ligand, and you want to treat both ligands as the "ligand" in
MM/PBSA. If the sequence is monomer-ligand-monomer-ligand, you will need to
specify your own ligand and receptor masks.
- Your prmtop files have different residue names for the same residue. For
instance, maybe the complex calls histidines "HIS" while the receptor has
them labeled as "HIE". (This is really a problem with prmtop generation in
my opinion, though).
So my advice is to take a look at some of your topology files that do not
work and see if you can determine why the algorithm it uses to detect the
receptor and ligand masks do not work. Hopefully it will be obvious why
such an approach would not work (and you then have to set receptor_mask and
ligand_mask by hand), or it reveals some kind of error in some of your
topology files.
HTH,
Jason
On Mon, Apr 25, 2016 at 6:29 PM, Martin Floor <martinfloor.gmail.com> wrote:
> Hello everybody:
>
> I am trying to run MMPBSA (3-trajectory) calculations and I encountered
> with an odd issue. I did simulate peptide-receptor interactions using the
> same receptor protein in combination with various different peptides. The
> simulation of the first peptide was analyzed without problems, but the
> other 11 complexes gave me an error:
>
> "PrmtopError: Couldn't predict mask from topology files!
> Your ligand residues must be sequential in your complex.
> There are likely problems with your topology files if this is not the
> case."
>
> This is very strange given that all simulations were produced with the same
> script that automates the process of file creations, and the only
> differences between simulations should be related to the peptide's
> aminoacidic sequence.
>
> The input for the script that I did use:
>
> *MMPBSA.py -O -i ../mmpbsa.in <http://mmpbsa.in> -o
> FINAL_RESULTS_MMPBSA.dat -sp rec_pep_solvated.prmtop -slp
> pep_solvated.prmtop -srp rec_solvated.prmtop -cp rec_pep.prmtop -rp
> rec.prmtop -lp pep.prmtop -y $(for ((j=1;j<=25;j++)); do ls
> ../../pep_$i/complex/rep_$j/prod_$j.mdcrd; done) -yl $(for
> ((j=1;j<=25;j++)); do ls ../../pep_$i/peptide/rep_$j/prod_$j.mdcrd; done)
> -yr $(for ((j=1;j<=25;j++)); do ls ../../receptor/rep_$j/prod_$j.mdcrd;
> done)*
>
> (The input considers 25 replicas of each complex (peptide-receptor)
> simulation and the "*for loops*" on the input are for calling them; *$i*
> call the peptides, pep_1 to pep_12 and *$j* call the replicas. I think this
> should not be relevant because the errors are related to the *.prmtop files
> read before the coordinate files)
>
> The input file for running PB (and GB) contains:
>
>
>
>
>
>
>
>
>
>
>
> *&general startframe=1, endframe=10000, interval=4, verbose=1,/&gb
> igb=2/&pb radiopt=0/*
> Looking for apparent reasons to explain why only the first peptide (i.e.
> pep_1) worked, I noticed that this complex is neutral by chance and did not
> required further ions to neutralize it. I am not sure if this could be the
> problem or if it is just coincidence. Given the first case, does anyone
> have an idea of how to fix this issue?
>
> Thanks in advance
>
> Martin.
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>
--
Jason M. Swails
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Received on Tue Apr 26 2016 - 06:00:03 PDT
