On Thu, Jun 23, 2016 at 10:50 AM, Shreeramesh <shreeramesh.gmail.com> wrote:
> Dear AMBER Users,
>
> I ran MMPBSA as per the script attached (mmpbsa-g.pbs and mmpbsa.in). It
> end up with the following error. Can you please help me to solve the error?
>
> Error:
>
> raise PrmtopError('Complex natom != receptor natom + ligand natom')
> PrmtopError: Complex natom != receptor natom + ligand natom
>
The error message is quite informative and tells you exactly what's
wrong. MM/PBSA is defined by subtracting the energies of the unbound state
conformations
from the energies of bound state conformations *for non-covalent binding
situations*. Naturally, then, the total number of atoms for the receptor
and ligand combined must be the same as the number of atoms in the
complex. In your case, this is not true. That is a problem you need to
fix.
HTH,
Jason
--
Jason M. Swails
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Received on Thu Jun 23 2016 - 10:30:02 PDT
