On Wed, Aug 31, 2022, laura zhang via AMBER wrote:
>
>I got the following error when using mmpbsa.py to calculate energy:
>
>Error: Number of atoms in NetCDF file (4560) does not match number
>Error: in associated topology (5295)!
>
>I think the reason is that I included water molecules in the protein mol2
>files before I solvated the system. The total number of atoms for the
>protein and ligand is 4560. If including the initial water molecules, then
>the total is 5295. I am wondering how to solve such kind of issue. Thank
>you!
Sounds like you may need to create the prmtop files needed "by hand",
removing all waters, not just those added by the solvateBox command. You
don't say how you created your prmtop files, but the "automated" procedures
cannot cover every possible situation. If you used cpptraj to strip waters,
then you can also create a prmtop file that corresponds to the NetCDF
trajectory file at that step.
...hope this helps....dac
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Received on Wed Aug 31 2022 - 07:00:04 PDT
