Hi,
Try specifying both receptor_mask=":1-614,662-669" and
ligand_mask=":615-661" in your mmpba.py input.
cheers,
Dwight
On Wed, Sep 28, 2016 at 9:06 AM, maryam azimzadehirani <
maryamai1988.gmail.com> wrote:
> 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?
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
T. Dwight McGee Jr.
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 28 2016 - 07:30:02 PDT
