Dear Amber users,
I am trying to calculate ligand-receptor binding energy. my receptor is
glycosylated. I generated the initial topology file with this order: 1.
Receptor 2.ligand 3.glycans. Then I ran simulation.
Now that I am trying to run binding energy calculation, I am getting this
error:
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
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.
Exiting. All files have been retained.
my input command line is:
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp com_sol.prmtop
-cp EGF_EGFR_no_wat.prmtop -rp EGFR_gly_no_wat.prmtop -lp EGF_no_wat.prmtop
-y *.mdcrd
where in the input file I specify the mask for the receptor residues as:
receptor_mask=:1-614,662-669
Can you please guide me on how to fix this issue? Is this due to the way
that I made the complex topology? or there is some other mistake in my
calculations?
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Received on Wed Sep 28 2016 - 06:30:04 PDT
