Hi Martin,
Without examining your topology files it is difficult to state what could
be causing the Map function in MMPBSA.py not determine the ligand and
receptor masks, if you prepared them correctly.
As a workaround you can manually specify the ligand and receptors masks
using the input variables, ligand_mask and receptor_mask in the &general
section.
Hope that Helps,
Dwight
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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>
--
T. Dwight McGee Jr.
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Mon Apr 25 2016 - 22:00:03 PDT
