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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Received on Mon Apr 25 2016 - 15:30:03 PDT
