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forlilab / waterkit

Tool to predict water molecules placement and energy in ligand binding sites
GNU General Public License v3.0
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Receptor preparation falied #15

Open khairbux2023 opened 2 months ago

khairbux2023 commented 2 months ago

I have run constant pH simulations with Gromacs and Now I want to trace the water molecules at different pH in my trajectory that processed in PDB format with last 1000 frames.

When I run receptor preparation command, I get the following error

**raise PDBError(f'Coordinate mismatch in model {self._current_model_number}')

parmed.exceptions.PDBError: Coordinate mismatch in model 1**

It seems that issue should be with Parmed and I have also added chain identifiers but still not working

diogomart commented 2 months ago

From waterkit's perspective you could process each frame independently.

If you are sure the error is raised by ParmEd, and it's not a known limitation for constant pH simulations, you could reach out to ParmEd developers.