On Tue, Oct 25, 2022, Amit Sharma (Asstt. Prof., MCARS) via AMBER wrote:
>Hello, I am trying to calculate the binding energy between the specific
>residue stretch (from residue :145-267) of the receptor with the ligand.
>The whole receptor is of 274 residue. While running the script it gave
>following error:
>PrmtopError: provided receptor/ligand masks don't select every atom in the
>complex topology!
This seems pretty clear, at least as far as Amber error messages go :-)
> receptor_mask=:145-267, ligand_mask=:275-298
The union of your receptor and ligand doesn't include the entire system, which
is what MMPBSA analysis requires.
Note that energy is not pairwise de-composable, so that there is no correct
answer to the question of what is the binding of just residues 145-267 to the
ligand. You could use decomposition analysis to get a rough idea of what
is going on.
Easier: strip residues 1-144 and 268-274 from each snapshot using cpptraj.
cpptraj can also provide a prmtop file corresponding to the smaller system.
Then use that for your MMPBSA analysis. This is also approximate, since you
are filling the space that used to be occupied by the stripped residues with
a high dielectric constant rather than a low one. But it may still provide
some insights.
...good luck...dac
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Received on Wed Oct 26 2022 - 05:30:05 PDT
